Module pycircos.pycircos
Expand source code
import os
import re
import io
import sys
import math
import urllib
import tempfile
import collections
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.path as mpath
import matplotlib.patches as mpatches
from Bio import SeqIO
import Bio
matplotlib.rcParams["figure.max_open_warning"] = 0
matplotlib.rcParams['ps.fonttype'] = 42
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['font.sans-serif'] = ["Arial","Lucida Sans","DejaVu Sans","Lucida Grande","Verdana"]
matplotlib.rcParams['font.family'] = 'sans-serif'
matplotlib.rcParams['font.size'] = 10.0
matplotlib.rcParams["axes.labelcolor"] = "#000000"
matplotlib.rcParams["axes.linewidth"] = 1.0
matplotlib.rcParams["xtick.major.width"] = 1.0
matplotlib.rcParams["ytick.major.width"] = 1.0
matplotlib.rcParams['xtick.major.pad'] = 6
matplotlib.rcParams['ytick.major.pad'] = 6
matplotlib.rcParams['xtick.major.size'] = 6
matplotlib.rcParams['ytick.major.size'] = 6
class Garc:
#list100 = ["#ffcdd2","#f8bbd0","#e1bee7","#d1c4e9","#c5cae9","#bbdefb","#b3e5fc","#b2ebf2","#b2dfdb","#c8e6c9","#dcedc8","#f0f4c3","#fff9c4","#ffecb3","#ffe0b2","#ffccbc","#d7ccc8","#cfd8dc",
colorlist = ["#ff8a80","#ff80ab","#ea80fc","#b388ff","#8c9eff","#82b1ff","#84ffff","#a7ffeb","#b9f6ca","#ccff90","#f4ff81","#ffff8d","#ffe57f","#ffd180","#ff9e80","#bcaaa4","#eeeeee","#b0bec5",
"#ff5252","#ff4081","#e040fb","#7c4dff","#536dfe","#448aff","#18ffff","#64ffda","#69f0ae","#b2ff59","#eeff41","#ffff00","#ffd740","#ffab40","#ff6e40","#a1887f","#e0e0e0","#90a4ae"]
_arcnum = 0
def __setitem__(self, key, item):
self.__dict__[key] = item
def __getitem__(self, key):
return self.__dict__[key]
def __init__(self, arc_id=None, record=None, size=1000, interspace=3, raxis_range=(500, 550), facecolor=None, edgecolor="#303030", linewidth=0.75, label=None, labelposition=0, labelsize=10, label_visible=False):
"""
Parameters
----------
arc_id : str, optional
Unique identifier for the Garc class object. In the event an id
value is not provided, an original unique ID is automatically
generated for Garc object. The default is None.
record : Bio.SeqRecord class object or NCBI accession number, optional
Bio.SeqRecord class object or NCBI accession number of an annotated
sequence. If a NCBI accession number is given, the GenBank record of
the accession number will be loaded from NCBI public database.
The default is None.
size : int, optional
Width of the arc section. If record is provided, the value is
instead set by the sequence length of the record. In reality
the actual arc section width in the resultant circle is determined
by the ratio of size to the combined sum of the size and interspace
values of the Garc class objects in the Gcircle class object.
The default is 1000.
interspace : float, optional
Distance angle (deg) to the adjacent arc section in clockwise
sequence. The actual interspace size in the circle is determined by
the actual arc section width in the resultant circle is determined
by the ratio of size to the combined sum of the size and interspace
values of the Garc class objects in the Gcircle class object.
The default is 3.
raxis_range : tuple (top=int, bottom=int), optional
Radial axis range where line plot is drawn. The default is (500, 550).
facecolor : str or tuple representing color code, optional
Color for filling. The default color is set automatically.
edgecolor : str or tuple representing color code, optional
Edge color of the filled area. The default is "#303030".
linewidth : float, optional
Edge line width. The default is 0.75.
label : str, optional
Label of the arc section. The default is None.
labelposition : int, optional
Relative label height from the center of the arc section.
The default is 0.
labelsize : int, optional
Font size of the label. The default is 10.
label_visible : bool, optional
If True, label of the Garc object is shown on the arc section.
The default is False.
Raises
------
ValueError
In the event no match for the NCBI accession number value input in
the record input variable, an error is raised.
Returns
-------
None
"""
self._parental_gcircle = None
if arc_id == None:
self.arc_id = str(Garc._arcnum)
else:
self.arc_id = arc_id
if record is None:
self.record = None
self.size = size
elif type(record) == Bio.SeqRecord.SeqRecord:
self.record = record
self.size = len(str(self.record.seq))
elif type(record) == str:
match = re.fullmatch("[a-zA-Z]{1,2}_?[0-9]{5,6}", record)
if os.path.exists(record) == True:
self.record = SeqIO.read(value, format="genbank")
if match is None:
raise ValueError("Incorrect value for NCBI accession number.")
else:
url = "https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=gbwithparts&id={}&withparts=on".format(record)
outb = io.BytesIO()
outs = io.StringIO()
headers = {"User-Agent": "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:47.0) Gecko/20100101 Firefox/47.0"}
request = urllib.request.Request(url, headers=headers)
with urllib.request.urlopen(request) as u:
outb.write(u.read())
outs.write(outb.getvalue().decode())
with tempfile.TemporaryFile(mode="w+") as o:
content = outs.getvalue()
o.write(content)
o.seek(0)
record = SeqIO.parse(o,"genbank")
record = next(record)
self.record = record
self.size = len(str(self.record.seq))
else:
self.record = None
self.size = size
if facecolor is None:
facecolor = Garc.colorlist[Garc._arcnum % len(Garc.colorlist)]
self.interspace = 2 * np.pi * (interspace / 360)
self.raxis_range = raxis_range
self.facecolor = facecolor
self.edgecolor = edgecolor
self.linewidth = linewidth
if label is None:
self.label = arc_id
else:
self.label = label
self.label_visible = label_visible
self.labelposition = labelposition
self.labelsize = labelsize
Garc._arcnum += 1
def calc_density(self, positions, window_size=1000):
"""
Converts positions consisting of x-coordinates into a list of density
values scanned in a sliding window.
Parameters
----------
positions : list of int or tuple
List of x coordinate values or tuple consisting of two x coordinate
values. Each coordinate value should be in the range 0 to the
size of Garc object.
window_size : int, optional
Size of the sliding window. The default is 1000.
Raises
------
ValueError
If an inappropriate value or values is input for positions, an
error is raised
Returns
-------
densities : list
A list consisting of density values.
"""
densities = []
positions.sort()
for i in range(0, self.size, window_size):
source = tuple(range(i, i+window_size))
amount = 0
for pos in positions:
if type(pos) == int:
if pos in source:
amount += 1
elif type(pos) == tuple:
if pos[0] <= source[-1] and pos[1] >= source[0]:
amount += 1
else:
raise ValueError("List elements should be int type or tuple consisting of two int values")
densities.append(amount)
source = tuple(range(i,self.size))
amount = 0
for pos in positions:
if type(pos) == int:
if pos in source:
amount += 1
elif type(pos) == tuple:
if pos[0] <= source[-1] and pos[1] >= source[0]:
amount += 1
else:
raise ValueError("List elements should be int type or tuple consisting of two int values")
densities.append(amount*((self.size-i)/window_size))
return densities
def calc_nnratio(self, n1="G", n2="C", window_size=1000, step_size=None):
"""
Calculates the ratio of n1 and n2 base frequency for multiple windows
along the sequence.
Parameters
----------
n1 : string corresponding to one of "ATGC", optional
The first of the two nucleotide bases to be compared.
The default is "G".
n2 : string corresponding to one of "ATGC", optional
The second of the two nucleotide bases to be compared.
The default is "C".
window_size : int, optional
Size of the sliding window. The default is 1000.
step_size : int, optional
Size of the sliding step. The default is window_size.
Raises
------
ValueError
In the event no record is provided, will return an error.
Returns
-------
gc_amounts : np.array
An array of the ratios computed by this method
"""
if self.record is None:
raise ValueError("self.record is None, please specify record value")
if step_size is None:
step_size = window_size
seq = str(self.record.seq)
gc_amounts = []
for i in range(0, len(seq), step_size):
if n2 is None:
gc_amount = seq[i:i+window_size].upper().count(n1) * 1.0 / window_size
else:
gc_amount = (seq[i:i+window_size].upper().count(n1) + seq[i:i+window_size].upper().count(n2)) * 1.0 / window_size
gc_amounts.append(gc_amount)
if n2 is None:
gc_amounts.append(seq[i:].upper().count(n1) * 1.0 / (len(seq)-i))
else:
gc_amounts.append((seq[i:].upper().count(n1) + seq[i:i+window_size].upper().count(n2)) * 1.0 / (len(seq)-i))
self["{}{}_ratio".format(n1,n2)] = gc_amounts
gc_amounts = np.array(gc_amounts)
return gc_amounts
def calc_nnskew(self, n1="G", n2="C", window_size=1000, step_size=None):
"""
Calculates n1,n2 skew (n1-n2)/(n1+n2) for multiple windows along
the sequence.
Parameters
----------
n1 : string corresponding to one of "ATGC", optional
The first of the two nucleotide bases to be compared.
The default is "G".
n2 : string corresponding to one of "ATGC", optional
The second of the two nucleotide bases to be compared.
The default is "C".
window_size : int, optional
Size of the sliding window. The default is 1000.
step_size : int, optional
Size of the sliding step. The default is window_size.
Raises
------
ValueError
In the event no record is provided, will return an error.
Returns
-------
gc_skews : np.array
An array of the skews computed by this method
"""
#(G-C)/(G+C)
if self.record is None:
raise ValueError("self.record is None, please specify record value")
if step_size is None:
step_size = window_size
seq = str(self.record.seq)
gc_skews = []
for i in range(0, len(seq), step_size):
gc_skew = (seq[i:i+window_size].upper().count(n1) - seq[i:i+window_size].upper().count(n2)) * 1.0 / (seq[i:i+window_size].upper().count(n1) + seq[i:i+window_size].upper().count(n2)) * 1.0
gc_skews.append(gc_skew)
gc_skews.append((seq[i:].upper().count(n1) - seq[i:].upper().count(n2)) * 1.0 / (seq[i:].upper().count(n1) + seq[i:].upper().count(n2)) * 1.0)
self["{}{}_skew".format(n1,n2)] = gc_skews
gc_skews = np.array(gc_skews)
return gc_skews
class Gcircle:
"""
A Gcircle class object provides a circle whose diameter is 1000 (a.u.) as a
drawing space. Any graph (line plot, scatter plot, barplot, heatmap, and chordplot)
can be placed on the space by specifying the raxis_range (from 0 to 1000) and
the corresponding Garc class object.
"""
colors = ["#f44336","#e91e63","#9c27b0","#673ab7","#3f51b5","#2196f3","#00bcd4","#009688","#4caf50","#8bc34a","#cddc39","#ffeb3b","#ffc107","#ff9800","#ff5722","#795548","#9e9e9e","#607d8b"]
#colors = ["#4E79A7","#F2BE2B","#E15759","#76B7B2","#59A14F","#EDC948","#B07AA1","#FF9DA7","#9C755F","#BAB0AC"]
cmaps = [plt.cm.Reds, plt.cm.Blues, plt.cm.Greens, plt.cm.Greys]
def __getattr__(self, name):
if name == "garc_dict":
return self._garc_dict
def __init__(self, fig=None, figsize=None):
"""
Parameters
----------
fig : matplotlib.pyplot.figure object, optional
Matplotlib Figure class object
figsize : tuple, optional
Figure size for the circular map
"""
self._garc_dict = {}
if fig is None:
if figsize is None:
figsize = (8,8)
self.figure = plt.figure(figsize=figsize)
self.fig_is_ext = False
else:
if figsize is None:
figsize = (6,6)
self.figure = fig
self.fig_is_ext = True
self.figsize = figsize
self.color_cycle = 0
def add_garc(self, garc):
"""
Add a new Garc class object into garc_dict.
Parameters
----------
garc : Garc class object
Garc class object to be added.
Returns
-------
None
"""
self._garc_dict[garc.arc_id] = garc
def set_garcs(self, start=0, end=360):
"""
Visualize the arc rectangles of the Garc class objects in .garc_dict on
the drawing space. After the execution of this method, a new Garc class
object cannot be added to garc_dict and figure parameter representing
maplotlib.pyplot.figure object will be created in Gcircle object.
Parameters
----------
start : int, optional
Start angle of the circos plot. The value range is -360 ~ 360.
The default is 0.
end : int, optional
End angle of the circos plot. The value range is -360 ~ 360.
The default is 360.
Returns
-------
None
"""
sum_length = sum(list(map(lambda x: self._garc_dict[x]["size"], list(self._garc_dict.keys()))))
sum_interspace = sum(list(map(lambda x: self._garc_dict[x]["interspace"], list(self._garc_dict.keys()))))
start = 2 * np.pi * start / 360
end = (2 * np.pi * end / 360) - sum_interspace
s = 0
sum_interspace = 0
for key in self._garc_dict.keys():
size = self._garc_dict[key].size
self._garc_dict[key].coordinates = [None, None]
self._garc_dict[key].coordinates[0] = sum_interspace + start + ((end-start) * s/sum_length) #self.theta_list[s:s+self._garc_dict[key]["size"]+1]
self._garc_dict[key].coordinates[1] = sum_interspace + start + ((end-start) * (s+size)/sum_length)
s = s + size
sum_interspace += self._garc_dict[key].interspace
#self.figure = plt.figure(figsize=self.figsize)
if self.fig_is_ext:
self.ax = self.figure.add_axes([0, 0, self.figsize[0], self.figsize[1]], polar=True)
else:
self.ax = self.figure.add_axes([0, 0, 1, 1], polar=True)
self.ax.set_theta_zero_location("N")
self.ax.set_theta_direction(-1)
self.ax.set_ylim(0,1000)
self.ax.spines['polar'].set_visible(False)
self.ax.xaxis.set_ticks([])
self.ax.xaxis.set_ticklabels([])
self.ax.yaxis.set_ticks([])
self.ax.yaxis.set_ticklabels([])
for i, key in enumerate(self._garc_dict.keys()):
pos = self._garc_dict[key].coordinates[0]
width = self._garc_dict[key].coordinates[-1] - self._garc_dict[key].coordinates[0]
height = abs(self._garc_dict[key].raxis_range[1] - self._garc_dict[key].raxis_range[0])
bottom = self._garc_dict[key].raxis_range[0]
facecolor = self._garc_dict[key].facecolor
edgecolor = self._garc_dict[key].edgecolor
linewidth = self._garc_dict[key].linewidth
#print(key, pos, pos+width)
self.ax.bar([pos], [height], bottom=bottom, width=width, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor, align="edge")
if self._garc_dict[key].label_visible == True:
rot = (self._garc_dict[key].coordinates[0] + self._garc_dict[key].coordinates[1]) / 2
rot = rot*360/(2*np.pi)
if 90 < rot < 270:
rot = 180-rot
else:
rot = -1 * rot
height = bottom + height/2 + self._garc_dict[key].labelposition
self.ax.text(pos + width/2, height, self._garc_dict[key].label, rotation=rot, ha="center", va="center", fontsize=self._garc_dict[key].labelsize)
def setspine(self, garc_id, raxis_range=(550, 600), facecolor="#30303000", edgecolor="#303030", linewidth=0.75):
"""
Set spines in the sector corresponding to the arc of
the Garc class object specified by garc_id.
Parameters
----------
garc_id : str
ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
raxis_range : tuple (top=int, bottom=int)
Radial axis range where line plot is drawn. The default is (550, 600).
facecolor : str or tuple representing color code, optional
Color for spines area. The default is "#30303000".
edgecolor : str or tuple representing color code, optional
Edge color of the spines boundary area. The default is "#303030".
linewidth : float, optional
Edge line width of spines boundary area. The default is 0.75.
Returns
-------
None
"""
pos = self._garc_dict[garc_id].coordinates[0]
width = self._garc_dict[garc_id].coordinates[-1] - self._garc_dict[garc_id].coordinates[0]
height = abs(raxis_range[1] - raxis_range[0])
bottom = raxis_range[0]
self.ax.bar([pos], [height], bottom=bottom, width=width, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor, align="edge", zorder=0)
def lineplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, linestyle="solid", linecolor=None, linewidth=1.0, spine=False):
"""
Plot a line in the sector corresponding to the arc of the Garc class
object specified by garc_id.
Parameters
----------
garc_id : str
ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data : list or numpy.ndarray
Numerical data to used for plot generation.
positions : list or numpy.ndarray
The x coordinates of the values in data on the Garc class object
when the plot is drawn on the rectangular coordinates. Each
coordinate value should be in the range 0 to size of the Garc class
object specified by garc_id. By the method execution, the
coordinates are converted to proper angle coordinates. If positions
are not given, proper coordinates values are generated according to
the length of data. The default is None.
raxis_range : tuple (top=int, bottom=int), optional
Radial axis range where line plot is drawn.
The default is (550, 600).
rlim : tuple (top=int, bottom=int)
The top and bottom r limits in data coordinates. If rlim value is
not given, the maximum value and the minimum value in data will be
set to top and bottom, respectively. The default is None.
linestyle : str, optional
Line style. The default is "solid".
Possible line styles are documented at
https://matplotlib.org/stable/gallery/lines_bars_and_markers/linestyles.html
linecolor : str or tuple representing color code, optional
Color of the line plot. If linecolor value is not given, the color
will be set according to the default color set of matplotlib. To
specify the opacity for a line color, please use `(r,g,b,a)` or
`#XXXXXXXX` format. The default is None.
linewidth : float, optional
Edge line width. The default is 1.0.
spine : bool, optional
If True, spines of the Garc object is shown on the arc section.
The default is False.
Returns
-------
None
"""
start = self._garc_dict[garc_id].coordinates[0]
end = self._garc_dict[garc_id].coordinates[-1]
size = self._garc_dict[garc_id].size - 1
positions_all = np.linspace(start, end, len(data), endpoint=True)
if positions is None:
positions = positions_all
else:
new_positions = []
for p in positions:
new_positions.append(start + ((end-start) * p/size))
positions = new_positions
if raxis_range is None:
raxis_range = raxis_range[0]
bottom = raxis_range[0]
top = raxis_range[1]
if linecolor is None:
linecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)]
self.color_cycle += 1
if rlim is None:
rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data)))
min_value = rlim[0]
max_value = rlim[1]
new_data = []
new_positions = []
new_data_array = []
new_positions_array = []
for p, v in zip(positions, data):
if v > rlim[1] or v < rlim[0]:
new_data_array.append(new_data)
new_positions_array.append(new_positions)
new_data = []
new_positions = []
else:
new_data.append(v)
new_positions.append(p)
new_data_array.append(new_data)
new_positions_array.append(new_positions)
for data, positions in zip(new_data_array, new_positions_array):
if len(positions) > 0:
data = np.array(data) - min_value
data = bottom + np.array(data * ((top - bottom) / (max_value - min_value)))
self.ax.plot(positions, data, color=linecolor, linewidth=linewidth, linestyle=linestyle)
if spine == True:
self.setspine(garc_id, raxis_range)
def fillplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, base_value=None, facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False):
"""
Fill a specified area in the sector corresponding to the arc of the
Garc class object specified by garc_id.
Parameters
----------
garc_id : str
ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data : list or numpy.ndarray
Numerical data to used for plot generation.
positions : list or numpy.ndarray
The x coordinates of the values in data on the Garc class object
when the plot is drawn on the rectangular coordinates. Each
coordinate value should be in the range 0 to size of the Garc class
object specified by garc_id. By the method execution, the
coordinates are converted to proper angle coordinates. If positions
are not given, proper coordinates values are generated according to
the length of data. The default is None.
raxis_range : tuple (top=int, bottom=int), optional
Radial axis range where line plot is drawn. The default is (550, 600).
rlim : tuple (top=int, bottom=int)
The top and bottom r limits in data coordinates. If rlim value is
not given, the maximum value and the minimum value in data will be
set to top and bottom, respectively.
The default is `(min(data), max(data))`.
base_value : float, optional
Base line height in data coordinates. The area between the base
line and the data line is filled by facecolor. The default is None.
facecolor : str or tuple representing color code, optional
Color for filling. The default is None.
edgecolor : str or tuple representing color code, optional
Edge color of the filled area. The default is "#303030".
linewidth : float, optional
Edge line width. The default is 0.0.
spine : bool, optional
If True, spines of the Garc object is shown on the arc section.
The default is False.
Returns
-------
None.
"""
start = self._garc_dict[garc_id].coordinates[0]
end = self._garc_dict[garc_id].coordinates[-1]
size = self._garc_dict[garc_id].size - 1
positions_all = np.linspace(start, end, len(data), endpoint=True)
if positions is None:
positions = positions_all
else:
new_positions = []
for p in positions:
new_positions.append(start + ((end-start) * p/size))
positions = new_positions
if raxis_range is None:
raxis_range = raxis_range[0]
bottom = raxis_range[0]
top = raxis_range[1]
if facecolor is None:
facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)]
self.color_cycle += 1
if rlim is None:
rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data)))
min_value = rlim[0]
max_value = rlim[1]
if base_value is None:
base_value = min_value
new_data = []
new_positions = []
new_data_array = []
new_positions_array = []
for p, v in zip(positions, data):
if v > rlim[1] or v < rlim[0]:
new_data_array.append(new_data)
new_positions_array.append(new_positions)
new_data = []
new_positions = []
else:
new_data.append(v)
new_positions.append(p)
new_data_array.append(new_data)
new_positions_array.append(new_positions)
for data, positions in zip(new_data_array, new_positions_array):
if len(positions) > 0:
base_value = base_value - min_value
base_value = bottom + base_value * ((top - bottom) / (max_value - min_value))
data = np.array(data) - min_value
data = bottom + np.array(data * ((top - bottom) / (max_value - min_value)))
self.ax.fill_between(positions, data, base_value, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor)
if spine == True:
self.setspine(garc_id, raxis_range)
def scatterplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, markershape="o", markersize=5, facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False):
"""
Plot markers in the sector corresponding to the arc of the Garc class
object specified by garc_id.
Parameters
----------
garc_id : str
ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data : list or numpy.ndarray
Numerical data to used for plot generation.
positions : list or numpy.ndarray
The x coordinates of the values in data on the Garc class object
when the plot is drawn on the rectangular coordinates. Each
coordinate value should be in the range 0 to size of the Garc class
object specified by garc_id. By the method execution, the
coordinates are converted to proper angle coordinates. If positions
are not given, proper coordinates values are generated according to
the length of data. The default is None.
raxis_range : tuple (top=int, bottom=int), optional
Radial axis range where line plot is drawn. The default is (550, 600).
rlim : tuple (top=int, bottom=int)
The top and bottom r limits in data coordinates. If rlim value is
not given, the maximum value and the minimum value in data will be
set to top and bottom, respectively.
The default is `(min(data), max(data))`.
markershape : str, optional
Marker shape. The default is "o".
Possible marker are listed at
https://matplotlib.org/stable/gallery/lines_bars_and_markers/marker_reference.html
markersize : float or list of float, optional
Size(s) of the marker(s). The default is 5.
facecolor : str or tuple representing color code or list thereof, optional
Face color(s) of the markers. If value type is list, the length of
facecolor should be the same as the data length.
The default is None.
edgecolor : str or tuple representing color code, optional
Edge color of the markers. The default is "#303030".
linewidth : float, optional
Edge line width of the markers. The default is 0.0.
spine : bool, optional
If True, spines of the Garc object is shown on the arc section.
The default is False.
Returns
-------
None
"""
start = self._garc_dict[garc_id].coordinates[0]
end = self._garc_dict[garc_id].coordinates[-1]
size = self._garc_dict[garc_id].size - 1
positions_all = np.linspace(start, end, len(data), endpoint=True)
if positions is None:
positions = positions_all
else:
new_positions = []
for p in positions:
new_positions.append(start + ((end-start) * p/size))
positions = new_positions
if raxis_range is None:
raxis_range = raxis_range[0]
bottom = raxis_range[0]
top = raxis_range[1]
if facecolor is None:
facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)]
self.color_cycle += 1
if rlim is None:
rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data)))
min_value = rlim[0]
max_value = rlim[1]
new_data = []
new_positions = []
new_data_array = []
new_positions_array = []
for p, v in zip(positions, data):
if v > rlim[1] or v < rlim[0]:
new_data_array.append(new_data)
new_positions_array.append(new_positions)
new_data = []
new_positions = []
else:
new_data.append(v)
new_positions.append(p)
new_data_array.append(new_data)
new_positions_array.append(new_positions)
for positions, data in zip(new_positions_array, new_data_array):
if len(positions) > 0:
data = np.array(data) - min_value
data = bottom + np.array(data * ((top - bottom) / (max_value - min_value)))
self.ax.scatter(positions, data, c=facecolor, s=markersize, linewidth=linewidth, edgecolor=edgecolor, marker=markershape)
if spine == True:
self.setspine(garc_id, raxis_range)
def barplot(self, garc_id, data, positions=None, width=None, raxis_range=(550, 600), rlim=None, base_value=None, facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False):
"""
Plot bars in the sector corresponding to the arc of the Garc class
object specified by garc_id.
Parameters
----------
garc_id : str
ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data : list or numpy.ndarray
Numerical data to used for plot generation.
positions : list or numpy.ndarray
The x coordinates of the values in data on the Garc class object
when the plot is drawn on the rectangular coordinates. Each
coordinate value should be in the range 0 to size of the Garc class
object specified by garc_id. By the method execution, the
coordinates are converted to proper angle coordinates. If positions
are not given, proper coordinates values are generated according to
the length of data. The default is None.
width : float or list of float
Width(s) of the bars. The default is `garc_object.size / len(data)`.
raxis_range : tuple (top=int, bottom=int), optional
Radial axis range where line plot is drawn. The default is (550, 600).
rlim : tuple (top=int, bottom=int)
The top and bottom r limits in data coordinates. If rlim value is
not given, the maximum value and the minimum value in data will be
set to top and bottom, respectively.
The default is (min(data), max(data).
base_value : float, optional
Base line height in data coordinates. The area between the base
line and the data line is filled by facecolor. The default is None.
facecolor : str or tuple representing color code or list thereof, optional
Facecolor(s) of the bars. If value type is list, the length of
facecolor should be the same as the data length.
The default is None.
edgecolor : str or tuple representing color code, optional
Edge color of the bars. The default is "#303030".
linewidth : float, optional
Edge line width of the bars. The default is 0.0.
spine : bool, optional
If True, spines of the Garc object is shown on the arc section.
The default is False.
Returns
-------
None
"""
start = self._garc_dict[garc_id].coordinates[0]
end = self._garc_dict[garc_id].coordinates[-1]
size = self._garc_dict[garc_id].size
positions_all = np.linspace(start, end, len(data), endpoint=False)
if positions is None:
positions = positions_all
else:
new_positions = []
for p in positions:
new_positions.append(start + ((end-start) * p/size))
positions = new_positions
if width is None:
width = [positions[1] - positions[0]] * len(data)
elif type(width) == float or type(width) == int:
width = [(end-start) * width/size] * len(data)
else:
new_width = []
for w in width:
new_w = (end-start) * w/size
new_width.append(new_w)
width = new_width
if raxis_range is None:
raxis_range = raxis_range[0]
bottom = raxis_range[0]
top = raxis_range[1]
if facecolor is None:
facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)]
self.color_cycle += 1
if rlim is None:
if min(data) != max(data):
rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data)))
else:
rlim = (min(data), max(data))
min_value = rlim[0] if rlim[0] is not None else min(data)
max_value = rlim[1] if rlim[1] is not None else max(data)
if base_value is None:
base_value = min_value
new_data = []
new_positions = []
new_width = []
new_data_array = []
new_positions_array = []
new_width_array = []
for p, v, w in zip(positions, data, width):
if v > rlim[1] or v < rlim[0]:
new_data_array.append(new_data)
new_positions_array.append(new_positions)
new_width_array.append(new_width)
new_data = []
new_width = []
new_positions = []
else:
new_data.append(v)
new_positions.append(p)
new_width.append(w)
new_data_array.append(new_data)
new_positions_array.append(new_positions)
new_width_array.append(new_width)
for data, positions, width in zip(new_data_array, new_positions_array, new_width_array):
if len(positions) > 0:
base_value = base_value - min_value
if min_value != max_value:
base_value = bottom + base_value * ((top - bottom) / (max_value - min_value))
else:
base_value = raxis_range[0]
data = np.array(data) - min_value
if min_value != max_value:
data = np.array(data) * ((top - bottom) / (max_value - min_value))
data = np.array(data) - (base_value - raxis_range[0])
else:
data = [raxis_range[1]-raxis_range[0]] * len(data)
self.ax.bar(positions, data, width=width, bottom=base_value, color=facecolor, linewidth=linewidth, edgecolor=edgecolor, align="edge")
if spine == True:
self.setspine(garc_id, raxis_range)
def heatmap(self, garc_id, data, positions=None, width=None, raxis_range=(550, 600), cmap=None, vmin=None, vmax=None, edgecolor="#303030", linewidth=0.0, spine=False):
"""
Visualize magnitudes of data values by color scale in the sector
corresponding to the arc of the Garc class object specified by garc_id.
Parameters
----------
garc_id : str
ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data : list or numpy.ndarray
Numerical data to used for plot generation.
positions : list or numpy.ndarray
The x coordinates of the values in data on the Garc class object
when the plot is drawn on the rectangular coordinates. Each
coordinate value should be in the range 0 to size of the Garc class
object specified by garc_id. By the method execution, the
coordinates are converted to proper angle coordinates. If positions
are not given, proper coordinates values are generated according to
the length of data. The default is None.
width : float or list of float, optional
Width(s) of the bars. The default is `garc_object.size / len(data)`.
raxis_range : tuple (top=int, bottom=int), optional
Radial axis range where heatmap is drawn. The default is (550, 600).
cmap : str representing matplotlib colormap name or
matplotlib.colors.Colormap object, optional
The mapping from data values to color space. The default is 'Reds'.
vmin : float, optional
Minimum data threshold for color scale. The default is min(data).
vmax : TYPE, optional
Maximum data threshold for color scale. The default is max(data).
edgecolor : str or tuple representing color code, optional
Edge color of the bars. The default is "#303030".
linewidth : float, optional
Edge line width of the bars. The default is 0.0.
spine : bool, optional
If True, spines of the Garc object is shown on the arc section.
The default is False.
Returns
-------
None
"""
start = self._garc_dict[garc_id].coordinates[0]
end = self._garc_dict[garc_id].coordinates[-1]
size = self._garc_dict[garc_id].size
positions_all = np.linspace(start, end, len(data), endpoint=False)
if positions is None:
positions = positions_all
else:
new_positions = []
for p in positions:
new_positions.append(start + ((end-start) * p/size))
positions = new_positions
if width is None:
width = [positions[1] - positions[0]] * len(data)
elif type(width) == float or type(width) == int:
width = [(end-start) * width/size] * len(data)
else:
new_width = []
for w in width:
new_w = (end-start) * w/size
new_width.append(new_w)
width = new_width
if raxis_range is None:
raxis_range = raxis_range[0]
bottom = raxis_range[0]
top = raxis_range[1]
height = top - bottom
if cmap is None:
cmap = Gcircle.cmaps[self.cmap_cycle % len(Gcircle.cmaps)]
self.cmap_cycle += 1
if vmax is None:
max_value = max(data)
else:
max_value = vmax
if vmin is None:
min_value = min(data)
else:
min_value = vmin
facecolors = []
for d in data:
facecolors.append(cmap(d/(max_value-min_value)))
self.ax.bar(positions, height=[height] * len(positions), width=width, bottom=bottom, color=facecolors, edgecolor=edgecolor, linewidth=linewidth, align="edge")
if spine == True:
self.setspine(garc_id, raxis_range)
def featureplot(self, garc_id, feature_type=None, source=None, raxis_range=(550, 600), facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False):
"""
Visualize sequence features with bar plots in the sector corresponding
to the arc of the Garc class object specified by garc_id.
Parameters
----------
garc_id : str
ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
feature_type : str, optional
Biological nature of the Bio.Seqfeature class objects (Any value is
acceptable, but GenBank format requires registering a biological
nature category for each sequence feature). If the value is "all",
all features in source will be drawn in the sector of the Garc
class object specified by grac_id. The default is 'all'.
source : list of Bio.SeqFeature object, optional
List of Bio.Seqfeature class object. If source value is not given,
record.features of the Garc class object specified by grac_id is
used. The default is record.features of the Garc class object
specified by grac_id.
raxis_range : tuple (top=int, bottom=int), optional
Radial axis range where feature plot is drawn. The default is (550, 600).
facecolor : str or tuple representing color code or list thereof, optional
Facecolor(s) of the bars. If value type is list, the length of
facecolor should be the same as the data length.
The default is None.
edgecolor : str or tuple representing color code, optional
Edge color of the bars. The default is "#303030".
linewidth : float, optional
Edge line width of the bars. The default is 0.0.
spine : bool, optional
If True, spines of the Garc object is shown on the arc section.
The default is False.
Returns
-------
None
"""
start = self._garc_dict[garc_id].coordinates[0]
end = self._garc_dict[garc_id].coordinates[-1]
size = self._garc_dict[garc_id].size - 1
if source is None:
source = self.record.features
if feature_type is None:
feature_list = source
else:
feature_list = [feat for feat in source if feat.type == feature_type]
positions = []
widths = []
for feat in feature_list:
if feat.location.strand >= 0:
s = int(feat.location.parts[0].start.position)
e = int(feat.location.parts[-1].end.position)
pos = start + ((end-start) * s/size)
width = start + ((end-start) * e/size) - pos
positions.append(pos)
widths.append(width)
else:
s = int(feat.location.parts[-1].start.position)
e = int(feat.location.parts[0].end.position)
pos = start + ((end-start) * s/size)
width = start + ((end-start) * e/size) - pos
positions.append(pos)
widths.append(width)
bottom = raxis_range[0]
top = raxis_range[1]
if facecolor is None:
facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)]
self.color_cycle += 1
self.ax.bar(positions, [abs(top-bottom)] * len(positions) , width=widths, bottom=bottom, color=facecolor, edgecolor=edgecolor, linewidth=linewidth, align="edge")
if spine == True:
self.setspine(garc_id, raxis_range)
def chord_plot(self, start_list, end_list, facecolor=None, edgecolor=None, linewidth=0.0):
"""
Visualize interrelationships between data.
Parameters
----------
start_list : tuple
Start data location of linked data.
The tuple is composed of four parameters:
- `arc_id` : `str`
The ID of the first Garc class object to be compared.
The ID should be in Gcircle object.garc_dict.
- `edge_position1` : `int`
The minimal x coordinates on the Garc class object
when the plot is drawn on the rectangular coordinates.
- `edge_position2` : `int`
The maximal x coordinates on the Garc class object
when the plot is drawn on the rectangular coordinates.
- `raxis_position` : `int`
The base height for the drawing chord.
end_list : tuple
End data location of linked data.
The tuple is composed of four parameters:
- `arc_id` : `str`
The ID of the second Garc class object to be compared.
The ID should be in Gcircle object.garc_dict.
- `edge_position1` : `int`
The minimal x coordinates on the Garc class object
when the plot is drawn on the rectangular coordinates.
- `edge_position2` : `int`
The maximal x coordinates on the Garc class object
when the plot is drawn on the rectangular coordinates.
- `raxis_position` : `int`
The base height for the drawing chord.
facecolor : str or tuple representing color code, optional
Facecolor of the link. The default is None.
edgecolor : str or tuple representing color code, optional
Edge color of the link. The default is "#303030".
linewidth : float, optional
Edge line width of the link. The default is 0.0.
Returns
-------
None
"""
garc_id1 = start_list[0]
garc_id2 = end_list[0]
center = 0
start1 = self._garc_dict[garc_id1].coordinates[0]
end1 = self._garc_dict[garc_id1].coordinates[-1]
size1 = self._garc_dict[garc_id1].size
sstart = start1 + ((end1-start1) * start_list[1]/size1)
send = start1 + ((end1-start1) * start_list[2]/size1)
stop = start_list[3]
start2 = self._garc_dict[garc_id2].coordinates[0]
end2 = self._garc_dict[garc_id2].coordinates[-1]
size2 = self._garc_dict[garc_id2].size
ostart = start2 + ((end2-start2) * end_list[1]/size2)
oend = start2 + ((end2-start2) * end_list[2]/size2)
etop = end_list[3]
if facecolor is None:
facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] + "80"
self.color_cycle += 1
z1 = stop - stop * math.cos(abs((send-sstart) * 0.5))
z2 = etop - etop * math.cos(abs((oend-ostart) * 0.5))
if sstart == ostart:
pass
else:
Path = mpath.Path
path_data = [(Path.MOVETO, (sstart, stop)),
(Path.CURVE3, (sstart, center)),
(Path.CURVE3, (oend, etop)),
(Path.CURVE3, ((ostart+oend)*0.5, etop+z2)),
(Path.CURVE3, (ostart, etop)),
(Path.CURVE3, (ostart, center)),
(Path.CURVE3, (send, stop)),
(Path.CURVE3, ((sstart+send)*0.5, stop+z1)),
(Path.CURVE3, (sstart, stop)),
]
codes, verts = list(zip(*path_data))
path = mpath.Path(verts, codes)
patch = mpatches.PathPatch(path, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor, zorder=0)
self.ax.add_patch(patch)
def tickplot(self, garc_id, raxis_range=None, tickinterval=1000, tickpositions=None, ticklabels=None, tickwidth=1, tickcolor="#303030", ticklabelsize=10, ticklabelcolor="#303030", ticklabelmargin=10, tickdirection="outer", ticklabelorientation="vertical"):
"""
Plot ticks on the arc of the Garc class object
Parameters
----------
garc_id : str
ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
raxis_range : tuple (top=int, bottom=int)
Radial axis range where tick plot is drawn.
If direction is "inner", the default is `(r0 - 0.5 * abs(r1 -r0), r0)`.
If direction is "outer", the default is `(r1, r1 + 0.5 * abs(r1 -r0))`.
`r0, r1 = Garc_object.raxis_range[0], Garc_object.raxis_range[1]`
tickinterval : int
Tick interval.
The default is 1000. If `tickpositions` value is given, this value will be ignored.
tickpositions : list of int
Positions on the arc of the Garc class object.
If you set ticks on your specified positions, please use this parameter instead of tickinterval
The values should be less than `Garc_object.size`.
ticklabels : list of int or list or str
Labels for ticks on the arc of the Garc class object.
The default is same with tickpositions.
tickwidth : float
Tick width. The default is 1.0.
tickcolor : str or float representing color code
Tick color. The default is "#303030"
ticklabelsize : float
Tick label fontsize. The default is 10.
ticklabelcolor : str
Tick label color, The default is "#303030".
ticklabelmargin : float
Tick label margin. The default is 10.
tickdirection : str ("outer" or "inner")
Tick direction. The default is "outer".
ticklabelorientation : str ("vertical" or "horizontal")
Tick label orientation. The default is "vertical".
Returns
-------
None
"""
start = self._garc_dict[garc_id].coordinates[0]
end = self._garc_dict[garc_id].coordinates[-1]
size = self._garc_dict[garc_id].size + 1
positions_all = np.linspace(start, end, size, endpoint=True)
if raxis_range is None:
r0, r1 = self._garc_dict[garc_id].raxis_range
tickheight = 0.5 * abs(r1 - r0)
if tickdirection == "outer":
raxis_range = (r1, r1 + tickheight)
elif tickdirection == "inner":
raxis_range = (r0 - tickheight, r0)
if tickpositions is None:
tickpositions = [pos for pos in range(0, size, tickinterval)]
if ticklabels is None:
ticklabels = [None] * len(tickpositions)
elif ticklabels == "None":
ticklabels = tickpositions
for pos, label in zip(tickpositions, ticklabels):
self.ax.plot([positions_all[pos], positions_all[pos]], raxis_range, linewidth=tickwidth, color=tickcolor)
if label is None:
pass
else:
ticklabel_rot = self._get_label_rotation(start + ((end - start) * (pos / size)), ticklabelorientation)
if ticklabelorientation == "horizontal":
label_width = ticklabelsize * 2
elif ticklabelorientation == "vertical":
label_width = ticklabelsize * len(str(label))
if tickdirection == "outer":
y_pos = raxis_range[1] + (label_width + ticklabelmargin)
elif tickdirection == "inner":
y_pos = raxis_range[0] - (label_width + ticklabelmargin)
self.ax.text(positions_all[pos], y_pos, str(label), rotation=ticklabel_rot, ha="center", va="center", fontsize=ticklabelsize, color=ticklabelcolor)
def _get_label_rotation(self, position, orientation="horizontal"):
"""
Get label rotation from label radian position
Parameters
----------
position : float
Label radian position (-2 * np.pi <= position <= 2 * np.pi)
orientation : str ("vertical" or "horizontal")
Label orientation, The default is "horizontal"
Returns
-------
rotation : float
Label rotation
"""
position_degree = position * (180 / np.pi) #-360 <= position_degree <= 360
if orientation == "horizontal":
rotation = 0 - position_degree
if -270 <= position_degree < -90 or 90 <= position_degree < 270:
rotation += 180
elif orientation == "vertical":
rotation = 90 - position_degree
if -180 <= position_degree < 0 or 180 <= position_degree < 360:
rotation += 180
return rotation
def save(self, file_name="test", format="pdf", dpi=None):
"""
Save image of Gcircle class figure object
Parameters
----------
file_name : str, optional
File name of figure. The default is "test".
format : str, optional
File format of figure. The default is "pdf"
dpi : int, optional
Dpi of figure. The default is None.
Returns
-------
None
"""
self.figure.patch.set_alpha(0.0)
if format == "pdf" and dpi is None:
self.figure.savefig(file_name + ".pdf", bbox_inches="tight")
else:
if dpi is None:
dpi = 600
self.figure.savefig(file_name + "." + format, bbox_inches="tight", dpi=dpi)
return self.figure
if __name__ == "__main__":
pass Classes
class Garc (arc_id=None, record=None, size=1000, interspace=3, raxis_range=(500, 550), facecolor=None, edgecolor='#303030', linewidth=0.75, label=None, labelposition=0, labelsize=10, label_visible=False)-
Parameters
arc_id:str, optional- Unique identifier for the Garc class object. In the event an id value is not provided, an original unique ID is automatically generated for Garc object. The default is None.
record:Bio.SeqRecord class objectorNCBI accession number, optional- Bio.SeqRecord class object or NCBI accession number of an annotated sequence. If a NCBI accession number is given, the GenBank record of the accession number will be loaded from NCBI public database. The default is None.
size:int, optional- Width of the arc section. If record is provided, the value is instead set by the sequence length of the record. In reality the actual arc section width in the resultant circle is determined by the ratio of size to the combined sum of the size and interspace values of the Garc class objects in the Gcircle class object. The default is 1000.
interspace:float, optional- Distance angle (deg) to the adjacent arc section in clockwise sequence. The actual interspace size in the circle is determined by the actual arc section width in the resultant circle is determined by the ratio of size to the combined sum of the size and interspace values of the Garc class objects in the Gcircle class object. The default is 3.
raxis_range:tuple (top=int, bottom=int), optional- Radial axis range where line plot is drawn. The default is (500, 550).
facecolor:strortuple representing color code, optional- Color for filling. The default color is set automatically.
edgecolor:strortuple representing color code, optional- Edge color of the filled area. The default is "#303030".
linewidth:float, optional- Edge line width. The default is 0.75.
label:str, optional- Label of the arc section. The default is None.
labelposition:int, optional- Relative label height from the center of the arc section. The default is 0.
labelsize:int, optional- Font size of the label. The default is 10.
label_visible:bool, optional- If True, label of the Garc object is shown on the arc section. The default is False.
Raises
ValueError- In the event no match for the NCBI accession number value input in the record input variable, an error is raised.
Returns
None
Expand source code
class Garc: #list100 = ["#ffcdd2","#f8bbd0","#e1bee7","#d1c4e9","#c5cae9","#bbdefb","#b3e5fc","#b2ebf2","#b2dfdb","#c8e6c9","#dcedc8","#f0f4c3","#fff9c4","#ffecb3","#ffe0b2","#ffccbc","#d7ccc8","#cfd8dc", colorlist = ["#ff8a80","#ff80ab","#ea80fc","#b388ff","#8c9eff","#82b1ff","#84ffff","#a7ffeb","#b9f6ca","#ccff90","#f4ff81","#ffff8d","#ffe57f","#ffd180","#ff9e80","#bcaaa4","#eeeeee","#b0bec5", "#ff5252","#ff4081","#e040fb","#7c4dff","#536dfe","#448aff","#18ffff","#64ffda","#69f0ae","#b2ff59","#eeff41","#ffff00","#ffd740","#ffab40","#ff6e40","#a1887f","#e0e0e0","#90a4ae"] _arcnum = 0 def __setitem__(self, key, item): self.__dict__[key] = item def __getitem__(self, key): return self.__dict__[key] def __init__(self, arc_id=None, record=None, size=1000, interspace=3, raxis_range=(500, 550), facecolor=None, edgecolor="#303030", linewidth=0.75, label=None, labelposition=0, labelsize=10, label_visible=False): """ Parameters ---------- arc_id : str, optional Unique identifier for the Garc class object. In the event an id value is not provided, an original unique ID is automatically generated for Garc object. The default is None. record : Bio.SeqRecord class object or NCBI accession number, optional Bio.SeqRecord class object or NCBI accession number of an annotated sequence. If a NCBI accession number is given, the GenBank record of the accession number will be loaded from NCBI public database. The default is None. size : int, optional Width of the arc section. If record is provided, the value is instead set by the sequence length of the record. In reality the actual arc section width in the resultant circle is determined by the ratio of size to the combined sum of the size and interspace values of the Garc class objects in the Gcircle class object. The default is 1000. interspace : float, optional Distance angle (deg) to the adjacent arc section in clockwise sequence. The actual interspace size in the circle is determined by the actual arc section width in the resultant circle is determined by the ratio of size to the combined sum of the size and interspace values of the Garc class objects in the Gcircle class object. The default is 3. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where line plot is drawn. The default is (500, 550). facecolor : str or tuple representing color code, optional Color for filling. The default color is set automatically. edgecolor : str or tuple representing color code, optional Edge color of the filled area. The default is "#303030". linewidth : float, optional Edge line width. The default is 0.75. label : str, optional Label of the arc section. The default is None. labelposition : int, optional Relative label height from the center of the arc section. The default is 0. labelsize : int, optional Font size of the label. The default is 10. label_visible : bool, optional If True, label of the Garc object is shown on the arc section. The default is False. Raises ------ ValueError In the event no match for the NCBI accession number value input in the record input variable, an error is raised. Returns ------- None """ self._parental_gcircle = None if arc_id == None: self.arc_id = str(Garc._arcnum) else: self.arc_id = arc_id if record is None: self.record = None self.size = size elif type(record) == Bio.SeqRecord.SeqRecord: self.record = record self.size = len(str(self.record.seq)) elif type(record) == str: match = re.fullmatch("[a-zA-Z]{1,2}_?[0-9]{5,6}", record) if os.path.exists(record) == True: self.record = SeqIO.read(value, format="genbank") if match is None: raise ValueError("Incorrect value for NCBI accession number.") else: url = "https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=gbwithparts&id={}&withparts=on".format(record) outb = io.BytesIO() outs = io.StringIO() headers = {"User-Agent": "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:47.0) Gecko/20100101 Firefox/47.0"} request = urllib.request.Request(url, headers=headers) with urllib.request.urlopen(request) as u: outb.write(u.read()) outs.write(outb.getvalue().decode()) with tempfile.TemporaryFile(mode="w+") as o: content = outs.getvalue() o.write(content) o.seek(0) record = SeqIO.parse(o,"genbank") record = next(record) self.record = record self.size = len(str(self.record.seq)) else: self.record = None self.size = size if facecolor is None: facecolor = Garc.colorlist[Garc._arcnum % len(Garc.colorlist)] self.interspace = 2 * np.pi * (interspace / 360) self.raxis_range = raxis_range self.facecolor = facecolor self.edgecolor = edgecolor self.linewidth = linewidth if label is None: self.label = arc_id else: self.label = label self.label_visible = label_visible self.labelposition = labelposition self.labelsize = labelsize Garc._arcnum += 1 def calc_density(self, positions, window_size=1000): """ Converts positions consisting of x-coordinates into a list of density values scanned in a sliding window. Parameters ---------- positions : list of int or tuple List of x coordinate values or tuple consisting of two x coordinate values. Each coordinate value should be in the range 0 to the size of Garc object. window_size : int, optional Size of the sliding window. The default is 1000. Raises ------ ValueError If an inappropriate value or values is input for positions, an error is raised Returns ------- densities : list A list consisting of density values. """ densities = [] positions.sort() for i in range(0, self.size, window_size): source = tuple(range(i, i+window_size)) amount = 0 for pos in positions: if type(pos) == int: if pos in source: amount += 1 elif type(pos) == tuple: if pos[0] <= source[-1] and pos[1] >= source[0]: amount += 1 else: raise ValueError("List elements should be int type or tuple consisting of two int values") densities.append(amount) source = tuple(range(i,self.size)) amount = 0 for pos in positions: if type(pos) == int: if pos in source: amount += 1 elif type(pos) == tuple: if pos[0] <= source[-1] and pos[1] >= source[0]: amount += 1 else: raise ValueError("List elements should be int type or tuple consisting of two int values") densities.append(amount*((self.size-i)/window_size)) return densities def calc_nnratio(self, n1="G", n2="C", window_size=1000, step_size=None): """ Calculates the ratio of n1 and n2 base frequency for multiple windows along the sequence. Parameters ---------- n1 : string corresponding to one of "ATGC", optional The first of the two nucleotide bases to be compared. The default is "G". n2 : string corresponding to one of "ATGC", optional The second of the two nucleotide bases to be compared. The default is "C". window_size : int, optional Size of the sliding window. The default is 1000. step_size : int, optional Size of the sliding step. The default is window_size. Raises ------ ValueError In the event no record is provided, will return an error. Returns ------- gc_amounts : np.array An array of the ratios computed by this method """ if self.record is None: raise ValueError("self.record is None, please specify record value") if step_size is None: step_size = window_size seq = str(self.record.seq) gc_amounts = [] for i in range(0, len(seq), step_size): if n2 is None: gc_amount = seq[i:i+window_size].upper().count(n1) * 1.0 / window_size else: gc_amount = (seq[i:i+window_size].upper().count(n1) + seq[i:i+window_size].upper().count(n2)) * 1.0 / window_size gc_amounts.append(gc_amount) if n2 is None: gc_amounts.append(seq[i:].upper().count(n1) * 1.0 / (len(seq)-i)) else: gc_amounts.append((seq[i:].upper().count(n1) + seq[i:i+window_size].upper().count(n2)) * 1.0 / (len(seq)-i)) self["{}{}_ratio".format(n1,n2)] = gc_amounts gc_amounts = np.array(gc_amounts) return gc_amounts def calc_nnskew(self, n1="G", n2="C", window_size=1000, step_size=None): """ Calculates n1,n2 skew (n1-n2)/(n1+n2) for multiple windows along the sequence. Parameters ---------- n1 : string corresponding to one of "ATGC", optional The first of the two nucleotide bases to be compared. The default is "G". n2 : string corresponding to one of "ATGC", optional The second of the two nucleotide bases to be compared. The default is "C". window_size : int, optional Size of the sliding window. The default is 1000. step_size : int, optional Size of the sliding step. The default is window_size. Raises ------ ValueError In the event no record is provided, will return an error. Returns ------- gc_skews : np.array An array of the skews computed by this method """ #(G-C)/(G+C) if self.record is None: raise ValueError("self.record is None, please specify record value") if step_size is None: step_size = window_size seq = str(self.record.seq) gc_skews = [] for i in range(0, len(seq), step_size): gc_skew = (seq[i:i+window_size].upper().count(n1) - seq[i:i+window_size].upper().count(n2)) * 1.0 / (seq[i:i+window_size].upper().count(n1) + seq[i:i+window_size].upper().count(n2)) * 1.0 gc_skews.append(gc_skew) gc_skews.append((seq[i:].upper().count(n1) - seq[i:].upper().count(n2)) * 1.0 / (seq[i:].upper().count(n1) + seq[i:].upper().count(n2)) * 1.0) self["{}{}_skew".format(n1,n2)] = gc_skews gc_skews = np.array(gc_skews) return gc_skewsSubclasses
Class variables
var colorlist
Methods
def calc_density(self, positions, window_size=1000)-
Converts positions consisting of x-coordinates into a list of density values scanned in a sliding window.
Parameters
positions:listofintortuple- List of x coordinate values or tuple consisting of two x coordinate values. Each coordinate value should be in the range 0 to the size of Garc object.
window_size:int, optional- Size of the sliding window. The default is 1000.
Raises
ValueError- If an inappropriate value or values is input for positions, an error is raised
Returns
densities:list- A list consisting of density values.
Expand source code
def calc_density(self, positions, window_size=1000): """ Converts positions consisting of x-coordinates into a list of density values scanned in a sliding window. Parameters ---------- positions : list of int or tuple List of x coordinate values or tuple consisting of two x coordinate values. Each coordinate value should be in the range 0 to the size of Garc object. window_size : int, optional Size of the sliding window. The default is 1000. Raises ------ ValueError If an inappropriate value or values is input for positions, an error is raised Returns ------- densities : list A list consisting of density values. """ densities = [] positions.sort() for i in range(0, self.size, window_size): source = tuple(range(i, i+window_size)) amount = 0 for pos in positions: if type(pos) == int: if pos in source: amount += 1 elif type(pos) == tuple: if pos[0] <= source[-1] and pos[1] >= source[0]: amount += 1 else: raise ValueError("List elements should be int type or tuple consisting of two int values") densities.append(amount) source = tuple(range(i,self.size)) amount = 0 for pos in positions: if type(pos) == int: if pos in source: amount += 1 elif type(pos) == tuple: if pos[0] <= source[-1] and pos[1] >= source[0]: amount += 1 else: raise ValueError("List elements should be int type or tuple consisting of two int values") densities.append(amount*((self.size-i)/window_size)) return densities def calc_nnratio(self, n1='G', n2='C', window_size=1000, step_size=None)-
Calculates the ratio of n1 and n2 base frequency for multiple windows along the sequence.
Parameters
n1:string corresponding to oneof"ATGC", optional- The first of the two nucleotide bases to be compared. The default is "G".
n2:string corresponding to oneof"ATGC", optional- The second of the two nucleotide bases to be compared. The default is "C".
window_size:int, optional- Size of the sliding window. The default is 1000.
step_size:int, optional- Size of the sliding step. The default is window_size.
Raises
ValueError- In the event no record is provided, will return an error.
Returns
gc_amounts:np.array- An array of the ratios computed by this method
Expand source code
def calc_nnratio(self, n1="G", n2="C", window_size=1000, step_size=None): """ Calculates the ratio of n1 and n2 base frequency for multiple windows along the sequence. Parameters ---------- n1 : string corresponding to one of "ATGC", optional The first of the two nucleotide bases to be compared. The default is "G". n2 : string corresponding to one of "ATGC", optional The second of the two nucleotide bases to be compared. The default is "C". window_size : int, optional Size of the sliding window. The default is 1000. step_size : int, optional Size of the sliding step. The default is window_size. Raises ------ ValueError In the event no record is provided, will return an error. Returns ------- gc_amounts : np.array An array of the ratios computed by this method """ if self.record is None: raise ValueError("self.record is None, please specify record value") if step_size is None: step_size = window_size seq = str(self.record.seq) gc_amounts = [] for i in range(0, len(seq), step_size): if n2 is None: gc_amount = seq[i:i+window_size].upper().count(n1) * 1.0 / window_size else: gc_amount = (seq[i:i+window_size].upper().count(n1) + seq[i:i+window_size].upper().count(n2)) * 1.0 / window_size gc_amounts.append(gc_amount) if n2 is None: gc_amounts.append(seq[i:].upper().count(n1) * 1.0 / (len(seq)-i)) else: gc_amounts.append((seq[i:].upper().count(n1) + seq[i:i+window_size].upper().count(n2)) * 1.0 / (len(seq)-i)) self["{}{}_ratio".format(n1,n2)] = gc_amounts gc_amounts = np.array(gc_amounts) return gc_amounts def calc_nnskew(self, n1='G', n2='C', window_size=1000, step_size=None)-
Calculates n1,n2 skew (n1-n2)/(n1+n2) for multiple windows along the sequence.
Parameters
n1:string corresponding to oneof"ATGC", optional- The first of the two nucleotide bases to be compared. The default is "G".
n2:string corresponding to oneof"ATGC", optional- The second of the two nucleotide bases to be compared. The default is "C".
window_size:int, optional- Size of the sliding window. The default is 1000.
step_size:int, optional- Size of the sliding step. The default is window_size.
Raises
ValueError- In the event no record is provided, will return an error.
Returns
gc_skews:np.array- An array of the skews computed by this method
Expand source code
def calc_nnskew(self, n1="G", n2="C", window_size=1000, step_size=None): """ Calculates n1,n2 skew (n1-n2)/(n1+n2) for multiple windows along the sequence. Parameters ---------- n1 : string corresponding to one of "ATGC", optional The first of the two nucleotide bases to be compared. The default is "G". n2 : string corresponding to one of "ATGC", optional The second of the two nucleotide bases to be compared. The default is "C". window_size : int, optional Size of the sliding window. The default is 1000. step_size : int, optional Size of the sliding step. The default is window_size. Raises ------ ValueError In the event no record is provided, will return an error. Returns ------- gc_skews : np.array An array of the skews computed by this method """ #(G-C)/(G+C) if self.record is None: raise ValueError("self.record is None, please specify record value") if step_size is None: step_size = window_size seq = str(self.record.seq) gc_skews = [] for i in range(0, len(seq), step_size): gc_skew = (seq[i:i+window_size].upper().count(n1) - seq[i:i+window_size].upper().count(n2)) * 1.0 / (seq[i:i+window_size].upper().count(n1) + seq[i:i+window_size].upper().count(n2)) * 1.0 gc_skews.append(gc_skew) gc_skews.append((seq[i:].upper().count(n1) - seq[i:].upper().count(n2)) * 1.0 / (seq[i:].upper().count(n1) + seq[i:].upper().count(n2)) * 1.0) self["{}{}_skew".format(n1,n2)] = gc_skews gc_skews = np.array(gc_skews) return gc_skews
class Gcircle (fig=None, figsize=None)-
A Gcircle class object provides a circle whose diameter is 1000 (a.u.) as a drawing space. Any graph (line plot, scatter plot, barplot, heatmap, and chordplot) can be placed on the space by specifying the raxis_range (from 0 to 1000) and the corresponding Garc class object.
Parameters
fig:matplotlib.pyplot.figure object, optional- Matplotlib Figure class object
figsize:tuple, optional- Figure size for the circular map
Expand source code
class Gcircle: """ A Gcircle class object provides a circle whose diameter is 1000 (a.u.) as a drawing space. Any graph (line plot, scatter plot, barplot, heatmap, and chordplot) can be placed on the space by specifying the raxis_range (from 0 to 1000) and the corresponding Garc class object. """ colors = ["#f44336","#e91e63","#9c27b0","#673ab7","#3f51b5","#2196f3","#00bcd4","#009688","#4caf50","#8bc34a","#cddc39","#ffeb3b","#ffc107","#ff9800","#ff5722","#795548","#9e9e9e","#607d8b"] #colors = ["#4E79A7","#F2BE2B","#E15759","#76B7B2","#59A14F","#EDC948","#B07AA1","#FF9DA7","#9C755F","#BAB0AC"] cmaps = [plt.cm.Reds, plt.cm.Blues, plt.cm.Greens, plt.cm.Greys] def __getattr__(self, name): if name == "garc_dict": return self._garc_dict def __init__(self, fig=None, figsize=None): """ Parameters ---------- fig : matplotlib.pyplot.figure object, optional Matplotlib Figure class object figsize : tuple, optional Figure size for the circular map """ self._garc_dict = {} if fig is None: if figsize is None: figsize = (8,8) self.figure = plt.figure(figsize=figsize) self.fig_is_ext = False else: if figsize is None: figsize = (6,6) self.figure = fig self.fig_is_ext = True self.figsize = figsize self.color_cycle = 0 def add_garc(self, garc): """ Add a new Garc class object into garc_dict. Parameters ---------- garc : Garc class object Garc class object to be added. Returns ------- None """ self._garc_dict[garc.arc_id] = garc def set_garcs(self, start=0, end=360): """ Visualize the arc rectangles of the Garc class objects in .garc_dict on the drawing space. After the execution of this method, a new Garc class object cannot be added to garc_dict and figure parameter representing maplotlib.pyplot.figure object will be created in Gcircle object. Parameters ---------- start : int, optional Start angle of the circos plot. The value range is -360 ~ 360. The default is 0. end : int, optional End angle of the circos plot. The value range is -360 ~ 360. The default is 360. Returns ------- None """ sum_length = sum(list(map(lambda x: self._garc_dict[x]["size"], list(self._garc_dict.keys())))) sum_interspace = sum(list(map(lambda x: self._garc_dict[x]["interspace"], list(self._garc_dict.keys())))) start = 2 * np.pi * start / 360 end = (2 * np.pi * end / 360) - sum_interspace s = 0 sum_interspace = 0 for key in self._garc_dict.keys(): size = self._garc_dict[key].size self._garc_dict[key].coordinates = [None, None] self._garc_dict[key].coordinates[0] = sum_interspace + start + ((end-start) * s/sum_length) #self.theta_list[s:s+self._garc_dict[key]["size"]+1] self._garc_dict[key].coordinates[1] = sum_interspace + start + ((end-start) * (s+size)/sum_length) s = s + size sum_interspace += self._garc_dict[key].interspace #self.figure = plt.figure(figsize=self.figsize) if self.fig_is_ext: self.ax = self.figure.add_axes([0, 0, self.figsize[0], self.figsize[1]], polar=True) else: self.ax = self.figure.add_axes([0, 0, 1, 1], polar=True) self.ax.set_theta_zero_location("N") self.ax.set_theta_direction(-1) self.ax.set_ylim(0,1000) self.ax.spines['polar'].set_visible(False) self.ax.xaxis.set_ticks([]) self.ax.xaxis.set_ticklabels([]) self.ax.yaxis.set_ticks([]) self.ax.yaxis.set_ticklabels([]) for i, key in enumerate(self._garc_dict.keys()): pos = self._garc_dict[key].coordinates[0] width = self._garc_dict[key].coordinates[-1] - self._garc_dict[key].coordinates[0] height = abs(self._garc_dict[key].raxis_range[1] - self._garc_dict[key].raxis_range[0]) bottom = self._garc_dict[key].raxis_range[0] facecolor = self._garc_dict[key].facecolor edgecolor = self._garc_dict[key].edgecolor linewidth = self._garc_dict[key].linewidth #print(key, pos, pos+width) self.ax.bar([pos], [height], bottom=bottom, width=width, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor, align="edge") if self._garc_dict[key].label_visible == True: rot = (self._garc_dict[key].coordinates[0] + self._garc_dict[key].coordinates[1]) / 2 rot = rot*360/(2*np.pi) if 90 < rot < 270: rot = 180-rot else: rot = -1 * rot height = bottom + height/2 + self._garc_dict[key].labelposition self.ax.text(pos + width/2, height, self._garc_dict[key].label, rotation=rot, ha="center", va="center", fontsize=self._garc_dict[key].labelsize) def setspine(self, garc_id, raxis_range=(550, 600), facecolor="#30303000", edgecolor="#303030", linewidth=0.75): """ Set spines in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. raxis_range : tuple (top=int, bottom=int) Radial axis range where line plot is drawn. The default is (550, 600). facecolor : str or tuple representing color code, optional Color for spines area. The default is "#30303000". edgecolor : str or tuple representing color code, optional Edge color of the spines boundary area. The default is "#303030". linewidth : float, optional Edge line width of spines boundary area. The default is 0.75. Returns ------- None """ pos = self._garc_dict[garc_id].coordinates[0] width = self._garc_dict[garc_id].coordinates[-1] - self._garc_dict[garc_id].coordinates[0] height = abs(raxis_range[1] - raxis_range[0]) bottom = raxis_range[0] self.ax.bar([pos], [height], bottom=bottom, width=width, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor, align="edge", zorder=0) def lineplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, linestyle="solid", linecolor=None, linewidth=1.0, spine=False): """ Plot a line in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where line plot is drawn. The default is (550, 600). rlim : tuple (top=int, bottom=int) The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is None. linestyle : str, optional Line style. The default is "solid". Possible line styles are documented at https://matplotlib.org/stable/gallery/lines_bars_and_markers/linestyles.html linecolor : str or tuple representing color code, optional Color of the line plot. If linecolor value is not given, the color will be set according to the default color set of matplotlib. To specify the opacity for a line color, please use `(r,g,b,a)` or `#XXXXXXXX` format. The default is None. linewidth : float, optional Edge line width. The default is 1.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size - 1 positions_all = np.linspace(start, end, len(data), endpoint=True) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] if linecolor is None: linecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 if rlim is None: rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data))) min_value = rlim[0] max_value = rlim[1] new_data = [] new_positions = [] new_data_array = [] new_positions_array = [] for p, v in zip(positions, data): if v > rlim[1] or v < rlim[0]: new_data_array.append(new_data) new_positions_array.append(new_positions) new_data = [] new_positions = [] else: new_data.append(v) new_positions.append(p) new_data_array.append(new_data) new_positions_array.append(new_positions) for data, positions in zip(new_data_array, new_positions_array): if len(positions) > 0: data = np.array(data) - min_value data = bottom + np.array(data * ((top - bottom) / (max_value - min_value))) self.ax.plot(positions, data, color=linecolor, linewidth=linewidth, linestyle=linestyle) if spine == True: self.setspine(garc_id, raxis_range) def fillplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, base_value=None, facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Fill a specified area in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where line plot is drawn. The default is (550, 600). rlim : tuple (top=int, bottom=int) The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is `(min(data), max(data))`. base_value : float, optional Base line height in data coordinates. The area between the base line and the data line is filled by facecolor. The default is None. facecolor : str or tuple representing color code, optional Color for filling. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the filled area. The default is "#303030". linewidth : float, optional Edge line width. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None. """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size - 1 positions_all = np.linspace(start, end, len(data), endpoint=True) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 if rlim is None: rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data))) min_value = rlim[0] max_value = rlim[1] if base_value is None: base_value = min_value new_data = [] new_positions = [] new_data_array = [] new_positions_array = [] for p, v in zip(positions, data): if v > rlim[1] or v < rlim[0]: new_data_array.append(new_data) new_positions_array.append(new_positions) new_data = [] new_positions = [] else: new_data.append(v) new_positions.append(p) new_data_array.append(new_data) new_positions_array.append(new_positions) for data, positions in zip(new_data_array, new_positions_array): if len(positions) > 0: base_value = base_value - min_value base_value = bottom + base_value * ((top - bottom) / (max_value - min_value)) data = np.array(data) - min_value data = bottom + np.array(data * ((top - bottom) / (max_value - min_value))) self.ax.fill_between(positions, data, base_value, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor) if spine == True: self.setspine(garc_id, raxis_range) def scatterplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, markershape="o", markersize=5, facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Plot markers in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where line plot is drawn. The default is (550, 600). rlim : tuple (top=int, bottom=int) The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is `(min(data), max(data))`. markershape : str, optional Marker shape. The default is "o". Possible marker are listed at https://matplotlib.org/stable/gallery/lines_bars_and_markers/marker_reference.html markersize : float or list of float, optional Size(s) of the marker(s). The default is 5. facecolor : str or tuple representing color code or list thereof, optional Face color(s) of the markers. If value type is list, the length of facecolor should be the same as the data length. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the markers. The default is "#303030". linewidth : float, optional Edge line width of the markers. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size - 1 positions_all = np.linspace(start, end, len(data), endpoint=True) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 if rlim is None: rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data))) min_value = rlim[0] max_value = rlim[1] new_data = [] new_positions = [] new_data_array = [] new_positions_array = [] for p, v in zip(positions, data): if v > rlim[1] or v < rlim[0]: new_data_array.append(new_data) new_positions_array.append(new_positions) new_data = [] new_positions = [] else: new_data.append(v) new_positions.append(p) new_data_array.append(new_data) new_positions_array.append(new_positions) for positions, data in zip(new_positions_array, new_data_array): if len(positions) > 0: data = np.array(data) - min_value data = bottom + np.array(data * ((top - bottom) / (max_value - min_value))) self.ax.scatter(positions, data, c=facecolor, s=markersize, linewidth=linewidth, edgecolor=edgecolor, marker=markershape) if spine == True: self.setspine(garc_id, raxis_range) def barplot(self, garc_id, data, positions=None, width=None, raxis_range=(550, 600), rlim=None, base_value=None, facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Plot bars in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. width : float or list of float Width(s) of the bars. The default is `garc_object.size / len(data)`. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where line plot is drawn. The default is (550, 600). rlim : tuple (top=int, bottom=int) The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is (min(data), max(data). base_value : float, optional Base line height in data coordinates. The area between the base line and the data line is filled by facecolor. The default is None. facecolor : str or tuple representing color code or list thereof, optional Facecolor(s) of the bars. If value type is list, the length of facecolor should be the same as the data length. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the bars. The default is "#303030". linewidth : float, optional Edge line width of the bars. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size positions_all = np.linspace(start, end, len(data), endpoint=False) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if width is None: width = [positions[1] - positions[0]] * len(data) elif type(width) == float or type(width) == int: width = [(end-start) * width/size] * len(data) else: new_width = [] for w in width: new_w = (end-start) * w/size new_width.append(new_w) width = new_width if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 if rlim is None: if min(data) != max(data): rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data))) else: rlim = (min(data), max(data)) min_value = rlim[0] if rlim[0] is not None else min(data) max_value = rlim[1] if rlim[1] is not None else max(data) if base_value is None: base_value = min_value new_data = [] new_positions = [] new_width = [] new_data_array = [] new_positions_array = [] new_width_array = [] for p, v, w in zip(positions, data, width): if v > rlim[1] or v < rlim[0]: new_data_array.append(new_data) new_positions_array.append(new_positions) new_width_array.append(new_width) new_data = [] new_width = [] new_positions = [] else: new_data.append(v) new_positions.append(p) new_width.append(w) new_data_array.append(new_data) new_positions_array.append(new_positions) new_width_array.append(new_width) for data, positions, width in zip(new_data_array, new_positions_array, new_width_array): if len(positions) > 0: base_value = base_value - min_value if min_value != max_value: base_value = bottom + base_value * ((top - bottom) / (max_value - min_value)) else: base_value = raxis_range[0] data = np.array(data) - min_value if min_value != max_value: data = np.array(data) * ((top - bottom) / (max_value - min_value)) data = np.array(data) - (base_value - raxis_range[0]) else: data = [raxis_range[1]-raxis_range[0]] * len(data) self.ax.bar(positions, data, width=width, bottom=base_value, color=facecolor, linewidth=linewidth, edgecolor=edgecolor, align="edge") if spine == True: self.setspine(garc_id, raxis_range) def heatmap(self, garc_id, data, positions=None, width=None, raxis_range=(550, 600), cmap=None, vmin=None, vmax=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Visualize magnitudes of data values by color scale in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. width : float or list of float, optional Width(s) of the bars. The default is `garc_object.size / len(data)`. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where heatmap is drawn. The default is (550, 600). cmap : str representing matplotlib colormap name or matplotlib.colors.Colormap object, optional The mapping from data values to color space. The default is 'Reds'. vmin : float, optional Minimum data threshold for color scale. The default is min(data). vmax : TYPE, optional Maximum data threshold for color scale. The default is max(data). edgecolor : str or tuple representing color code, optional Edge color of the bars. The default is "#303030". linewidth : float, optional Edge line width of the bars. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size positions_all = np.linspace(start, end, len(data), endpoint=False) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if width is None: width = [positions[1] - positions[0]] * len(data) elif type(width) == float or type(width) == int: width = [(end-start) * width/size] * len(data) else: new_width = [] for w in width: new_w = (end-start) * w/size new_width.append(new_w) width = new_width if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] height = top - bottom if cmap is None: cmap = Gcircle.cmaps[self.cmap_cycle % len(Gcircle.cmaps)] self.cmap_cycle += 1 if vmax is None: max_value = max(data) else: max_value = vmax if vmin is None: min_value = min(data) else: min_value = vmin facecolors = [] for d in data: facecolors.append(cmap(d/(max_value-min_value))) self.ax.bar(positions, height=[height] * len(positions), width=width, bottom=bottom, color=facecolors, edgecolor=edgecolor, linewidth=linewidth, align="edge") if spine == True: self.setspine(garc_id, raxis_range) def featureplot(self, garc_id, feature_type=None, source=None, raxis_range=(550, 600), facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Visualize sequence features with bar plots in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. feature_type : str, optional Biological nature of the Bio.Seqfeature class objects (Any value is acceptable, but GenBank format requires registering a biological nature category for each sequence feature). If the value is "all", all features in source will be drawn in the sector of the Garc class object specified by grac_id. The default is 'all'. source : list of Bio.SeqFeature object, optional List of Bio.Seqfeature class object. If source value is not given, record.features of the Garc class object specified by grac_id is used. The default is record.features of the Garc class object specified by grac_id. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where feature plot is drawn. The default is (550, 600). facecolor : str or tuple representing color code or list thereof, optional Facecolor(s) of the bars. If value type is list, the length of facecolor should be the same as the data length. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the bars. The default is "#303030". linewidth : float, optional Edge line width of the bars. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size - 1 if source is None: source = self.record.features if feature_type is None: feature_list = source else: feature_list = [feat for feat in source if feat.type == feature_type] positions = [] widths = [] for feat in feature_list: if feat.location.strand >= 0: s = int(feat.location.parts[0].start.position) e = int(feat.location.parts[-1].end.position) pos = start + ((end-start) * s/size) width = start + ((end-start) * e/size) - pos positions.append(pos) widths.append(width) else: s = int(feat.location.parts[-1].start.position) e = int(feat.location.parts[0].end.position) pos = start + ((end-start) * s/size) width = start + ((end-start) * e/size) - pos positions.append(pos) widths.append(width) bottom = raxis_range[0] top = raxis_range[1] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 self.ax.bar(positions, [abs(top-bottom)] * len(positions) , width=widths, bottom=bottom, color=facecolor, edgecolor=edgecolor, linewidth=linewidth, align="edge") if spine == True: self.setspine(garc_id, raxis_range) def chord_plot(self, start_list, end_list, facecolor=None, edgecolor=None, linewidth=0.0): """ Visualize interrelationships between data. Parameters ---------- start_list : tuple Start data location of linked data. The tuple is composed of four parameters: - `arc_id` : `str` The ID of the first Garc class object to be compared. The ID should be in Gcircle object.garc_dict. - `edge_position1` : `int` The minimal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates. - `edge_position2` : `int` The maximal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates. - `raxis_position` : `int` The base height for the drawing chord. end_list : tuple End data location of linked data. The tuple is composed of four parameters: - `arc_id` : `str` The ID of the second Garc class object to be compared. The ID should be in Gcircle object.garc_dict. - `edge_position1` : `int` The minimal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates. - `edge_position2` : `int` The maximal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates. - `raxis_position` : `int` The base height for the drawing chord. facecolor : str or tuple representing color code, optional Facecolor of the link. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the link. The default is "#303030". linewidth : float, optional Edge line width of the link. The default is 0.0. Returns ------- None """ garc_id1 = start_list[0] garc_id2 = end_list[0] center = 0 start1 = self._garc_dict[garc_id1].coordinates[0] end1 = self._garc_dict[garc_id1].coordinates[-1] size1 = self._garc_dict[garc_id1].size sstart = start1 + ((end1-start1) * start_list[1]/size1) send = start1 + ((end1-start1) * start_list[2]/size1) stop = start_list[3] start2 = self._garc_dict[garc_id2].coordinates[0] end2 = self._garc_dict[garc_id2].coordinates[-1] size2 = self._garc_dict[garc_id2].size ostart = start2 + ((end2-start2) * end_list[1]/size2) oend = start2 + ((end2-start2) * end_list[2]/size2) etop = end_list[3] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] + "80" self.color_cycle += 1 z1 = stop - stop * math.cos(abs((send-sstart) * 0.5)) z2 = etop - etop * math.cos(abs((oend-ostart) * 0.5)) if sstart == ostart: pass else: Path = mpath.Path path_data = [(Path.MOVETO, (sstart, stop)), (Path.CURVE3, (sstart, center)), (Path.CURVE3, (oend, etop)), (Path.CURVE3, ((ostart+oend)*0.5, etop+z2)), (Path.CURVE3, (ostart, etop)), (Path.CURVE3, (ostart, center)), (Path.CURVE3, (send, stop)), (Path.CURVE3, ((sstart+send)*0.5, stop+z1)), (Path.CURVE3, (sstart, stop)), ] codes, verts = list(zip(*path_data)) path = mpath.Path(verts, codes) patch = mpatches.PathPatch(path, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor, zorder=0) self.ax.add_patch(patch) def tickplot(self, garc_id, raxis_range=None, tickinterval=1000, tickpositions=None, ticklabels=None, tickwidth=1, tickcolor="#303030", ticklabelsize=10, ticklabelcolor="#303030", ticklabelmargin=10, tickdirection="outer", ticklabelorientation="vertical"): """ Plot ticks on the arc of the Garc class object Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. raxis_range : tuple (top=int, bottom=int) Radial axis range where tick plot is drawn. If direction is "inner", the default is `(r0 - 0.5 * abs(r1 -r0), r0)`. If direction is "outer", the default is `(r1, r1 + 0.5 * abs(r1 -r0))`. `r0, r1 = Garc_object.raxis_range[0], Garc_object.raxis_range[1]` tickinterval : int Tick interval. The default is 1000. If `tickpositions` value is given, this value will be ignored. tickpositions : list of int Positions on the arc of the Garc class object. If you set ticks on your specified positions, please use this parameter instead of tickinterval The values should be less than `Garc_object.size`. ticklabels : list of int or list or str Labels for ticks on the arc of the Garc class object. The default is same with tickpositions. tickwidth : float Tick width. The default is 1.0. tickcolor : str or float representing color code Tick color. The default is "#303030" ticklabelsize : float Tick label fontsize. The default is 10. ticklabelcolor : str Tick label color, The default is "#303030". ticklabelmargin : float Tick label margin. The default is 10. tickdirection : str ("outer" or "inner") Tick direction. The default is "outer". ticklabelorientation : str ("vertical" or "horizontal") Tick label orientation. The default is "vertical". Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size + 1 positions_all = np.linspace(start, end, size, endpoint=True) if raxis_range is None: r0, r1 = self._garc_dict[garc_id].raxis_range tickheight = 0.5 * abs(r1 - r0) if tickdirection == "outer": raxis_range = (r1, r1 + tickheight) elif tickdirection == "inner": raxis_range = (r0 - tickheight, r0) if tickpositions is None: tickpositions = [pos for pos in range(0, size, tickinterval)] if ticklabels is None: ticklabels = [None] * len(tickpositions) elif ticklabels == "None": ticklabels = tickpositions for pos, label in zip(tickpositions, ticklabels): self.ax.plot([positions_all[pos], positions_all[pos]], raxis_range, linewidth=tickwidth, color=tickcolor) if label is None: pass else: ticklabel_rot = self._get_label_rotation(start + ((end - start) * (pos / size)), ticklabelorientation) if ticklabelorientation == "horizontal": label_width = ticklabelsize * 2 elif ticklabelorientation == "vertical": label_width = ticklabelsize * len(str(label)) if tickdirection == "outer": y_pos = raxis_range[1] + (label_width + ticklabelmargin) elif tickdirection == "inner": y_pos = raxis_range[0] - (label_width + ticklabelmargin) self.ax.text(positions_all[pos], y_pos, str(label), rotation=ticklabel_rot, ha="center", va="center", fontsize=ticklabelsize, color=ticklabelcolor) def _get_label_rotation(self, position, orientation="horizontal"): """ Get label rotation from label radian position Parameters ---------- position : float Label radian position (-2 * np.pi <= position <= 2 * np.pi) orientation : str ("vertical" or "horizontal") Label orientation, The default is "horizontal" Returns ------- rotation : float Label rotation """ position_degree = position * (180 / np.pi) #-360 <= position_degree <= 360 if orientation == "horizontal": rotation = 0 - position_degree if -270 <= position_degree < -90 or 90 <= position_degree < 270: rotation += 180 elif orientation == "vertical": rotation = 90 - position_degree if -180 <= position_degree < 0 or 180 <= position_degree < 360: rotation += 180 return rotation def save(self, file_name="test", format="pdf", dpi=None): """ Save image of Gcircle class figure object Parameters ---------- file_name : str, optional File name of figure. The default is "test". format : str, optional File format of figure. The default is "pdf" dpi : int, optional Dpi of figure. The default is None. Returns ------- None """ self.figure.patch.set_alpha(0.0) if format == "pdf" and dpi is None: self.figure.savefig(file_name + ".pdf", bbox_inches="tight") else: if dpi is None: dpi = 600 self.figure.savefig(file_name + "." + format, bbox_inches="tight", dpi=dpi) return self.figureSubclasses
Class variables
var colorsvar cmaps
Methods
def add_garc(self, garc)-
Add a new Garc class object into garc_dict.
Parameters
garc:Garc class object- Garc class object to be added.
Returns
None
Expand source code
def add_garc(self, garc): """ Add a new Garc class object into garc_dict. Parameters ---------- garc : Garc class object Garc class object to be added. Returns ------- None """ self._garc_dict[garc.arc_id] = garc def set_garcs(self, start=0, end=360)-
Visualize the arc rectangles of the Garc class objects in .garc_dict on the drawing space. After the execution of this method, a new Garc class object cannot be added to garc_dict and figure parameter representing maplotlib.pyplot.figure object will be created in Gcircle object.
Parameters
start:int, optional- Start angle of the circos plot. The value range is -360 ~ 360. The default is 0.
end:int, optional- End angle of the circos plot. The value range is -360 ~ 360. The default is 360.
Returns
None
Expand source code
def set_garcs(self, start=0, end=360): """ Visualize the arc rectangles of the Garc class objects in .garc_dict on the drawing space. After the execution of this method, a new Garc class object cannot be added to garc_dict and figure parameter representing maplotlib.pyplot.figure object will be created in Gcircle object. Parameters ---------- start : int, optional Start angle of the circos plot. The value range is -360 ~ 360. The default is 0. end : int, optional End angle of the circos plot. The value range is -360 ~ 360. The default is 360. Returns ------- None """ sum_length = sum(list(map(lambda x: self._garc_dict[x]["size"], list(self._garc_dict.keys())))) sum_interspace = sum(list(map(lambda x: self._garc_dict[x]["interspace"], list(self._garc_dict.keys())))) start = 2 * np.pi * start / 360 end = (2 * np.pi * end / 360) - sum_interspace s = 0 sum_interspace = 0 for key in self._garc_dict.keys(): size = self._garc_dict[key].size self._garc_dict[key].coordinates = [None, None] self._garc_dict[key].coordinates[0] = sum_interspace + start + ((end-start) * s/sum_length) #self.theta_list[s:s+self._garc_dict[key]["size"]+1] self._garc_dict[key].coordinates[1] = sum_interspace + start + ((end-start) * (s+size)/sum_length) s = s + size sum_interspace += self._garc_dict[key].interspace #self.figure = plt.figure(figsize=self.figsize) if self.fig_is_ext: self.ax = self.figure.add_axes([0, 0, self.figsize[0], self.figsize[1]], polar=True) else: self.ax = self.figure.add_axes([0, 0, 1, 1], polar=True) self.ax.set_theta_zero_location("N") self.ax.set_theta_direction(-1) self.ax.set_ylim(0,1000) self.ax.spines['polar'].set_visible(False) self.ax.xaxis.set_ticks([]) self.ax.xaxis.set_ticklabels([]) self.ax.yaxis.set_ticks([]) self.ax.yaxis.set_ticklabels([]) for i, key in enumerate(self._garc_dict.keys()): pos = self._garc_dict[key].coordinates[0] width = self._garc_dict[key].coordinates[-1] - self._garc_dict[key].coordinates[0] height = abs(self._garc_dict[key].raxis_range[1] - self._garc_dict[key].raxis_range[0]) bottom = self._garc_dict[key].raxis_range[0] facecolor = self._garc_dict[key].facecolor edgecolor = self._garc_dict[key].edgecolor linewidth = self._garc_dict[key].linewidth #print(key, pos, pos+width) self.ax.bar([pos], [height], bottom=bottom, width=width, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor, align="edge") if self._garc_dict[key].label_visible == True: rot = (self._garc_dict[key].coordinates[0] + self._garc_dict[key].coordinates[1]) / 2 rot = rot*360/(2*np.pi) if 90 < rot < 270: rot = 180-rot else: rot = -1 * rot height = bottom + height/2 + self._garc_dict[key].labelposition self.ax.text(pos + width/2, height, self._garc_dict[key].label, rotation=rot, ha="center", va="center", fontsize=self._garc_dict[key].labelsize) def setspine(self, garc_id, raxis_range=(550, 600), facecolor='#30303000', edgecolor='#303030', linewidth=0.75)-
Set spines in the sector corresponding to the arc of the Garc class object specified by garc_id.
Parameters
garc_id:str- ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
raxis_range:tuple (top=int, bottom=int)- Radial axis range where line plot is drawn. The default is (550, 600).
facecolor:strortuple representing color code, optional- Color for spines area. The default is "#30303000".
edgecolor:strortuple representing color code, optional- Edge color of the spines boundary area. The default is "#303030".
linewidth:float, optional- Edge line width of spines boundary area. The default is 0.75.
Returns
None
Expand source code
def setspine(self, garc_id, raxis_range=(550, 600), facecolor="#30303000", edgecolor="#303030", linewidth=0.75): """ Set spines in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. raxis_range : tuple (top=int, bottom=int) Radial axis range where line plot is drawn. The default is (550, 600). facecolor : str or tuple representing color code, optional Color for spines area. The default is "#30303000". edgecolor : str or tuple representing color code, optional Edge color of the spines boundary area. The default is "#303030". linewidth : float, optional Edge line width of spines boundary area. The default is 0.75. Returns ------- None """ pos = self._garc_dict[garc_id].coordinates[0] width = self._garc_dict[garc_id].coordinates[-1] - self._garc_dict[garc_id].coordinates[0] height = abs(raxis_range[1] - raxis_range[0]) bottom = raxis_range[0] self.ax.bar([pos], [height], bottom=bottom, width=width, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor, align="edge", zorder=0) def lineplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, linestyle='solid', linecolor=None, linewidth=1.0, spine=False)-
Plot a line in the sector corresponding to the arc of the Garc class object specified by garc_id.
Parameters
garc_id:str- ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data:listornumpy.ndarray- Numerical data to used for plot generation.
positions:listornumpy.ndarray- The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None.
raxis_range:tuple (top=int, bottom=int), optional- Radial axis range where line plot is drawn. The default is (550, 600).
rlim:tuple (top=int, bottom=int)- The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is None.
linestyle:str, optional- Line style. The default is "solid". Possible line styles are documented at https://matplotlib.org/stable/gallery/lines_bars_and_markers/linestyles.html
linecolor:strortuple representing color code, optional- Color of the line plot. If linecolor value is not given, the color
will be set according to the default color set of matplotlib. To
specify the opacity for a line color, please use
(r,g,b,a)or#XXXXXXXXformat. The default is None. linewidth:float, optional- Edge line width. The default is 1.0.
spine:bool, optional- If True, spines of the Garc object is shown on the arc section. The default is False.
Returns
None
Expand source code
def lineplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, linestyle="solid", linecolor=None, linewidth=1.0, spine=False): """ Plot a line in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where line plot is drawn. The default is (550, 600). rlim : tuple (top=int, bottom=int) The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is None. linestyle : str, optional Line style. The default is "solid". Possible line styles are documented at https://matplotlib.org/stable/gallery/lines_bars_and_markers/linestyles.html linecolor : str or tuple representing color code, optional Color of the line plot. If linecolor value is not given, the color will be set according to the default color set of matplotlib. To specify the opacity for a line color, please use `(r,g,b,a)` or `#XXXXXXXX` format. The default is None. linewidth : float, optional Edge line width. The default is 1.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size - 1 positions_all = np.linspace(start, end, len(data), endpoint=True) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] if linecolor is None: linecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 if rlim is None: rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data))) min_value = rlim[0] max_value = rlim[1] new_data = [] new_positions = [] new_data_array = [] new_positions_array = [] for p, v in zip(positions, data): if v > rlim[1] or v < rlim[0]: new_data_array.append(new_data) new_positions_array.append(new_positions) new_data = [] new_positions = [] else: new_data.append(v) new_positions.append(p) new_data_array.append(new_data) new_positions_array.append(new_positions) for data, positions in zip(new_data_array, new_positions_array): if len(positions) > 0: data = np.array(data) - min_value data = bottom + np.array(data * ((top - bottom) / (max_value - min_value))) self.ax.plot(positions, data, color=linecolor, linewidth=linewidth, linestyle=linestyle) if spine == True: self.setspine(garc_id, raxis_range) def fillplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, base_value=None, facecolor=None, edgecolor='#303030', linewidth=0.0, spine=False)-
Fill a specified area in the sector corresponding to the arc of the Garc class object specified by garc_id.
Parameters
garc_id:str- ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data:listornumpy.ndarray- Numerical data to used for plot generation.
positions:listornumpy.ndarray- The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None.
raxis_range:tuple (top=int, bottom=int), optional- Radial axis range where line plot is drawn. The default is (550, 600).
rlim:tuple (top=int, bottom=int)- The top and bottom r limits in data coordinates. If rlim value is
not given, the maximum value and the minimum value in data will be
set to top and bottom, respectively.
The default is
(min(data), max(data)). base_value:float, optional- Base line height in data coordinates. The area between the base line and the data line is filled by facecolor. The default is None.
facecolor:strortuple representing color code, optional- Color for filling. The default is None.
edgecolor:strortuple representing color code, optional- Edge color of the filled area. The default is "#303030".
linewidth:float, optional- Edge line width. The default is 0.0.
spine:bool, optional- If True, spines of the Garc object is shown on the arc section. The default is False.
Returns
None.
Expand source code
def fillplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, base_value=None, facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Fill a specified area in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where line plot is drawn. The default is (550, 600). rlim : tuple (top=int, bottom=int) The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is `(min(data), max(data))`. base_value : float, optional Base line height in data coordinates. The area between the base line and the data line is filled by facecolor. The default is None. facecolor : str or tuple representing color code, optional Color for filling. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the filled area. The default is "#303030". linewidth : float, optional Edge line width. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None. """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size - 1 positions_all = np.linspace(start, end, len(data), endpoint=True) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 if rlim is None: rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data))) min_value = rlim[0] max_value = rlim[1] if base_value is None: base_value = min_value new_data = [] new_positions = [] new_data_array = [] new_positions_array = [] for p, v in zip(positions, data): if v > rlim[1] or v < rlim[0]: new_data_array.append(new_data) new_positions_array.append(new_positions) new_data = [] new_positions = [] else: new_data.append(v) new_positions.append(p) new_data_array.append(new_data) new_positions_array.append(new_positions) for data, positions in zip(new_data_array, new_positions_array): if len(positions) > 0: base_value = base_value - min_value base_value = bottom + base_value * ((top - bottom) / (max_value - min_value)) data = np.array(data) - min_value data = bottom + np.array(data * ((top - bottom) / (max_value - min_value))) self.ax.fill_between(positions, data, base_value, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor) if spine == True: self.setspine(garc_id, raxis_range) def scatterplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, markershape='o', markersize=5, facecolor=None, edgecolor='#303030', linewidth=0.0, spine=False)-
Plot markers in the sector corresponding to the arc of the Garc class object specified by garc_id.
Parameters
garc_id:str- ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data:listornumpy.ndarray- Numerical data to used for plot generation.
positions:listornumpy.ndarray- The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None.
raxis_range:tuple (top=int, bottom=int), optional- Radial axis range where line plot is drawn. The default is (550, 600).
rlim:tuple (top=int, bottom=int)- The top and bottom r limits in data coordinates. If rlim value is
not given, the maximum value and the minimum value in data will be
set to top and bottom, respectively.
The default is
(min(data), max(data)). markershape:str, optional- Marker shape. The default is "o". Possible marker are listed at https://matplotlib.org/stable/gallery/lines_bars_and_markers/marker_reference.html
markersize:floatorlistoffloat, optional- Size(s) of the marker(s). The default is 5.
facecolor:strortuple representing color codeorlist thereof, optional- Face color(s) of the markers. If value type is list, the length of facecolor should be the same as the data length. The default is None.
edgecolor:strortuple representing color code, optional- Edge color of the markers. The default is "#303030".
linewidth:float, optional- Edge line width of the markers. The default is 0.0.
spine:bool, optional- If True, spines of the Garc object is shown on the arc section. The default is False.
Returns
None
Expand source code
def scatterplot(self, garc_id, data, positions=None, raxis_range=(550, 600), rlim=None, markershape="o", markersize=5, facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Plot markers in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where line plot is drawn. The default is (550, 600). rlim : tuple (top=int, bottom=int) The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is `(min(data), max(data))`. markershape : str, optional Marker shape. The default is "o". Possible marker are listed at https://matplotlib.org/stable/gallery/lines_bars_and_markers/marker_reference.html markersize : float or list of float, optional Size(s) of the marker(s). The default is 5. facecolor : str or tuple representing color code or list thereof, optional Face color(s) of the markers. If value type is list, the length of facecolor should be the same as the data length. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the markers. The default is "#303030". linewidth : float, optional Edge line width of the markers. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size - 1 positions_all = np.linspace(start, end, len(data), endpoint=True) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 if rlim is None: rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data))) min_value = rlim[0] max_value = rlim[1] new_data = [] new_positions = [] new_data_array = [] new_positions_array = [] for p, v in zip(positions, data): if v > rlim[1] or v < rlim[0]: new_data_array.append(new_data) new_positions_array.append(new_positions) new_data = [] new_positions = [] else: new_data.append(v) new_positions.append(p) new_data_array.append(new_data) new_positions_array.append(new_positions) for positions, data in zip(new_positions_array, new_data_array): if len(positions) > 0: data = np.array(data) - min_value data = bottom + np.array(data * ((top - bottom) / (max_value - min_value))) self.ax.scatter(positions, data, c=facecolor, s=markersize, linewidth=linewidth, edgecolor=edgecolor, marker=markershape) if spine == True: self.setspine(garc_id, raxis_range) def barplot(self, garc_id, data, positions=None, width=None, raxis_range=(550, 600), rlim=None, base_value=None, facecolor=None, edgecolor='#303030', linewidth=0.0, spine=False)-
Plot bars in the sector corresponding to the arc of the Garc class object specified by garc_id.
Parameters
garc_id:str- ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data:listornumpy.ndarray- Numerical data to used for plot generation.
positions:listornumpy.ndarray- The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None.
width:floatorlistoffloat- Width(s) of the bars. The default is
garc_object.size / len(data). raxis_range:tuple (top=int, bottom=int), optional- Radial axis range where line plot is drawn. The default is (550, 600).
rlim:tuple (top=int, bottom=int)- The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is (min(data), max(data).
base_value:float, optional- Base line height in data coordinates. The area between the base line and the data line is filled by facecolor. The default is None.
facecolor:strortuple representing color codeorlist thereof, optional- Facecolor(s) of the bars. If value type is list, the length of facecolor should be the same as the data length. The default is None.
edgecolor:strortuple representing color code, optional- Edge color of the bars. The default is "#303030".
linewidth:float, optional- Edge line width of the bars. The default is 0.0.
spine:bool, optional- If True, spines of the Garc object is shown on the arc section. The default is False.
Returns
None
Expand source code
def barplot(self, garc_id, data, positions=None, width=None, raxis_range=(550, 600), rlim=None, base_value=None, facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Plot bars in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. width : float or list of float Width(s) of the bars. The default is `garc_object.size / len(data)`. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where line plot is drawn. The default is (550, 600). rlim : tuple (top=int, bottom=int) The top and bottom r limits in data coordinates. If rlim value is not given, the maximum value and the minimum value in data will be set to top and bottom, respectively. The default is (min(data), max(data). base_value : float, optional Base line height in data coordinates. The area between the base line and the data line is filled by facecolor. The default is None. facecolor : str or tuple representing color code or list thereof, optional Facecolor(s) of the bars. If value type is list, the length of facecolor should be the same as the data length. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the bars. The default is "#303030". linewidth : float, optional Edge line width of the bars. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size positions_all = np.linspace(start, end, len(data), endpoint=False) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if width is None: width = [positions[1] - positions[0]] * len(data) elif type(width) == float or type(width) == int: width = [(end-start) * width/size] * len(data) else: new_width = [] for w in width: new_w = (end-start) * w/size new_width.append(new_w) width = new_width if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 if rlim is None: if min(data) != max(data): rlim = (min(data) - 0.05 * abs(min(data)), max(data) + 0.05 * abs(max(data))) else: rlim = (min(data), max(data)) min_value = rlim[0] if rlim[0] is not None else min(data) max_value = rlim[1] if rlim[1] is not None else max(data) if base_value is None: base_value = min_value new_data = [] new_positions = [] new_width = [] new_data_array = [] new_positions_array = [] new_width_array = [] for p, v, w in zip(positions, data, width): if v > rlim[1] or v < rlim[0]: new_data_array.append(new_data) new_positions_array.append(new_positions) new_width_array.append(new_width) new_data = [] new_width = [] new_positions = [] else: new_data.append(v) new_positions.append(p) new_width.append(w) new_data_array.append(new_data) new_positions_array.append(new_positions) new_width_array.append(new_width) for data, positions, width in zip(new_data_array, new_positions_array, new_width_array): if len(positions) > 0: base_value = base_value - min_value if min_value != max_value: base_value = bottom + base_value * ((top - bottom) / (max_value - min_value)) else: base_value = raxis_range[0] data = np.array(data) - min_value if min_value != max_value: data = np.array(data) * ((top - bottom) / (max_value - min_value)) data = np.array(data) - (base_value - raxis_range[0]) else: data = [raxis_range[1]-raxis_range[0]] * len(data) self.ax.bar(positions, data, width=width, bottom=base_value, color=facecolor, linewidth=linewidth, edgecolor=edgecolor, align="edge") if spine == True: self.setspine(garc_id, raxis_range) def heatmap(self, garc_id, data, positions=None, width=None, raxis_range=(550, 600), cmap=None, vmin=None, vmax=None, edgecolor='#303030', linewidth=0.0, spine=False)-
Visualize magnitudes of data values by color scale in the sector corresponding to the arc of the Garc class object specified by garc_id.
Parameters
garc_id:str- ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
data:listornumpy.ndarray- Numerical data to used for plot generation.
positions:listornumpy.ndarray- The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None.
width:floatorlistoffloat, optional- Width(s) of the bars. The default is
garc_object.size / len(data). raxis_range:tuple (top=int, bottom=int), optional- Radial axis range where heatmap is drawn. The default is (550, 600).
cmap:str representing matplotlib colormap name or- matplotlib.colors.Colormap object, optional The mapping from data values to color space. The default is 'Reds'.
vmin:float, optional- Minimum data threshold for color scale. The default is min(data).
vmax:TYPE, optional- Maximum data threshold for color scale. The default is max(data).
edgecolor:strortuple representing color code, optional- Edge color of the bars. The default is "#303030".
linewidth:float, optional- Edge line width of the bars. The default is 0.0.
spine:bool, optional- If True, spines of the Garc object is shown on the arc section. The default is False.
Returns
None
Expand source code
def heatmap(self, garc_id, data, positions=None, width=None, raxis_range=(550, 600), cmap=None, vmin=None, vmax=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Visualize magnitudes of data values by color scale in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. data : list or numpy.ndarray Numerical data to used for plot generation. positions : list or numpy.ndarray The x coordinates of the values in data on the Garc class object when the plot is drawn on the rectangular coordinates. Each coordinate value should be in the range 0 to size of the Garc class object specified by garc_id. By the method execution, the coordinates are converted to proper angle coordinates. If positions are not given, proper coordinates values are generated according to the length of data. The default is None. width : float or list of float, optional Width(s) of the bars. The default is `garc_object.size / len(data)`. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where heatmap is drawn. The default is (550, 600). cmap : str representing matplotlib colormap name or matplotlib.colors.Colormap object, optional The mapping from data values to color space. The default is 'Reds'. vmin : float, optional Minimum data threshold for color scale. The default is min(data). vmax : TYPE, optional Maximum data threshold for color scale. The default is max(data). edgecolor : str or tuple representing color code, optional Edge color of the bars. The default is "#303030". linewidth : float, optional Edge line width of the bars. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size positions_all = np.linspace(start, end, len(data), endpoint=False) if positions is None: positions = positions_all else: new_positions = [] for p in positions: new_positions.append(start + ((end-start) * p/size)) positions = new_positions if width is None: width = [positions[1] - positions[0]] * len(data) elif type(width) == float or type(width) == int: width = [(end-start) * width/size] * len(data) else: new_width = [] for w in width: new_w = (end-start) * w/size new_width.append(new_w) width = new_width if raxis_range is None: raxis_range = raxis_range[0] bottom = raxis_range[0] top = raxis_range[1] height = top - bottom if cmap is None: cmap = Gcircle.cmaps[self.cmap_cycle % len(Gcircle.cmaps)] self.cmap_cycle += 1 if vmax is None: max_value = max(data) else: max_value = vmax if vmin is None: min_value = min(data) else: min_value = vmin facecolors = [] for d in data: facecolors.append(cmap(d/(max_value-min_value))) self.ax.bar(positions, height=[height] * len(positions), width=width, bottom=bottom, color=facecolors, edgecolor=edgecolor, linewidth=linewidth, align="edge") if spine == True: self.setspine(garc_id, raxis_range) def featureplot(self, garc_id, feature_type=None, source=None, raxis_range=(550, 600), facecolor=None, edgecolor='#303030', linewidth=0.0, spine=False)-
Visualize sequence features with bar plots in the sector corresponding to the arc of the Garc class object specified by garc_id.
Parameters
garc_id:str- ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
feature_type:str, optional- Biological nature of the Bio.Seqfeature class objects (Any value is acceptable, but GenBank format requires registering a biological nature category for each sequence feature). If the value is "all", all features in source will be drawn in the sector of the Garc class object specified by grac_id. The default is 'all'.
source:listofBio.SeqFeature object, optional- List of Bio.Seqfeature class object. If source value is not given, record.features of the Garc class object specified by grac_id is used. The default is record.features of the Garc class object specified by grac_id.
raxis_range:tuple (top=int, bottom=int), optional- Radial axis range where feature plot is drawn. The default is (550, 600).
facecolor:strortuple representing color codeorlist thereof, optional- Facecolor(s) of the bars. If value type is list, the length of facecolor should be the same as the data length. The default is None.
edgecolor:strortuple representing color code, optional- Edge color of the bars. The default is "#303030".
linewidth:float, optional- Edge line width of the bars. The default is 0.0.
spine:bool, optional- If True, spines of the Garc object is shown on the arc section. The default is False.
Returns
None
Expand source code
def featureplot(self, garc_id, feature_type=None, source=None, raxis_range=(550, 600), facecolor=None, edgecolor="#303030", linewidth=0.0, spine=False): """ Visualize sequence features with bar plots in the sector corresponding to the arc of the Garc class object specified by garc_id. Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. feature_type : str, optional Biological nature of the Bio.Seqfeature class objects (Any value is acceptable, but GenBank format requires registering a biological nature category for each sequence feature). If the value is "all", all features in source will be drawn in the sector of the Garc class object specified by grac_id. The default is 'all'. source : list of Bio.SeqFeature object, optional List of Bio.Seqfeature class object. If source value is not given, record.features of the Garc class object specified by grac_id is used. The default is record.features of the Garc class object specified by grac_id. raxis_range : tuple (top=int, bottom=int), optional Radial axis range where feature plot is drawn. The default is (550, 600). facecolor : str or tuple representing color code or list thereof, optional Facecolor(s) of the bars. If value type is list, the length of facecolor should be the same as the data length. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the bars. The default is "#303030". linewidth : float, optional Edge line width of the bars. The default is 0.0. spine : bool, optional If True, spines of the Garc object is shown on the arc section. The default is False. Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size - 1 if source is None: source = self.record.features if feature_type is None: feature_list = source else: feature_list = [feat for feat in source if feat.type == feature_type] positions = [] widths = [] for feat in feature_list: if feat.location.strand >= 0: s = int(feat.location.parts[0].start.position) e = int(feat.location.parts[-1].end.position) pos = start + ((end-start) * s/size) width = start + ((end-start) * e/size) - pos positions.append(pos) widths.append(width) else: s = int(feat.location.parts[-1].start.position) e = int(feat.location.parts[0].end.position) pos = start + ((end-start) * s/size) width = start + ((end-start) * e/size) - pos positions.append(pos) widths.append(width) bottom = raxis_range[0] top = raxis_range[1] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] self.color_cycle += 1 self.ax.bar(positions, [abs(top-bottom)] * len(positions) , width=widths, bottom=bottom, color=facecolor, edgecolor=edgecolor, linewidth=linewidth, align="edge") if spine == True: self.setspine(garc_id, raxis_range) def chord_plot(self, start_list, end_list, facecolor=None, edgecolor=None, linewidth=0.0)-
Visualize interrelationships between data.
Parameters
start_list:tuple-
Start data location of linked data.
The tuple is composed of four parameters:arc_id:str
The ID of the first Garc class object to be compared. The ID should be in Gcircle object.garc_dict.edge_position1:int
The minimal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates.edge_position2:int
The maximal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates.raxis_position:int
The base height for the drawing chord.
end_list:tuple-
End data location of linked data.
The tuple is composed of four parameters:arc_id:str
The ID of the second Garc class object to be compared. The ID should be in Gcircle object.garc_dict.edge_position1:int
The minimal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates.edge_position2:int
The maximal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates.raxis_position:int
The base height for the drawing chord.
facecolor:strortuple representing color code, optional- Facecolor of the link. The default is None.
edgecolor:strortuple representing color code, optional- Edge color of the link. The default is "#303030".
linewidth:float, optional- Edge line width of the link. The default is 0.0.
Returns
None
Expand source code
def chord_plot(self, start_list, end_list, facecolor=None, edgecolor=None, linewidth=0.0): """ Visualize interrelationships between data. Parameters ---------- start_list : tuple Start data location of linked data. The tuple is composed of four parameters: - `arc_id` : `str` The ID of the first Garc class object to be compared. The ID should be in Gcircle object.garc_dict. - `edge_position1` : `int` The minimal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates. - `edge_position2` : `int` The maximal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates. - `raxis_position` : `int` The base height for the drawing chord. end_list : tuple End data location of linked data. The tuple is composed of four parameters: - `arc_id` : `str` The ID of the second Garc class object to be compared. The ID should be in Gcircle object.garc_dict. - `edge_position1` : `int` The minimal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates. - `edge_position2` : `int` The maximal x coordinates on the Garc class object when the plot is drawn on the rectangular coordinates. - `raxis_position` : `int` The base height for the drawing chord. facecolor : str or tuple representing color code, optional Facecolor of the link. The default is None. edgecolor : str or tuple representing color code, optional Edge color of the link. The default is "#303030". linewidth : float, optional Edge line width of the link. The default is 0.0. Returns ------- None """ garc_id1 = start_list[0] garc_id2 = end_list[0] center = 0 start1 = self._garc_dict[garc_id1].coordinates[0] end1 = self._garc_dict[garc_id1].coordinates[-1] size1 = self._garc_dict[garc_id1].size sstart = start1 + ((end1-start1) * start_list[1]/size1) send = start1 + ((end1-start1) * start_list[2]/size1) stop = start_list[3] start2 = self._garc_dict[garc_id2].coordinates[0] end2 = self._garc_dict[garc_id2].coordinates[-1] size2 = self._garc_dict[garc_id2].size ostart = start2 + ((end2-start2) * end_list[1]/size2) oend = start2 + ((end2-start2) * end_list[2]/size2) etop = end_list[3] if facecolor is None: facecolor = Gcircle.colors[self.color_cycle % len(Gcircle.colors)] + "80" self.color_cycle += 1 z1 = stop - stop * math.cos(abs((send-sstart) * 0.5)) z2 = etop - etop * math.cos(abs((oend-ostart) * 0.5)) if sstart == ostart: pass else: Path = mpath.Path path_data = [(Path.MOVETO, (sstart, stop)), (Path.CURVE3, (sstart, center)), (Path.CURVE3, (oend, etop)), (Path.CURVE3, ((ostart+oend)*0.5, etop+z2)), (Path.CURVE3, (ostart, etop)), (Path.CURVE3, (ostart, center)), (Path.CURVE3, (send, stop)), (Path.CURVE3, ((sstart+send)*0.5, stop+z1)), (Path.CURVE3, (sstart, stop)), ] codes, verts = list(zip(*path_data)) path = mpath.Path(verts, codes) patch = mpatches.PathPatch(path, facecolor=facecolor, linewidth=linewidth, edgecolor=edgecolor, zorder=0) self.ax.add_patch(patch) def tickplot(self, garc_id, raxis_range=None, tickinterval=1000, tickpositions=None, ticklabels=None, tickwidth=1, tickcolor='#303030', ticklabelsize=10, ticklabelcolor='#303030', ticklabelmargin=10, tickdirection='outer', ticklabelorientation='vertical')-
Plot ticks on the arc of the Garc class object
Parameters
garc_id:str- ID of the Garc class object. The ID should be in Gcircle object.garc_dict.
raxis_range:tuple (top=int, bottom=int)- Radial axis range where tick plot is drawn.
If direction is "inner", the default is(r0 - 0.5 * abs(r1 -r0), r0).
If direction is "outer", the default is(r1, r1 + 0.5 * abs(r1 -r0)).
r0, r1 = Garc_object.raxis_range[0], Garc_object.raxis_range[1] tickinterval:int- Tick interval.
The default is 1000. If
tickpositionsvalue is given, this value will be ignored. tickpositions:listofint- Positions on the arc of the Garc class object.
If you set ticks on your specified positions, please use this parameter instead of tickinterval
The values should be less than
Garc_object.size. ticklabels:listofintorlistorstr- Labels for ticks on the arc of the Garc class object. The default is same with tickpositions.
tickwidth:float- Tick width. The default is 1.0.
tickcolor:strorfloat representing color code- Tick color. The default is "#303030"
ticklabelsize:float- Tick label fontsize. The default is 10.
ticklabelcolor:str- Tick label color, The default is "#303030".
ticklabelmargin:float- Tick label margin. The default is 10.
tickdirection:str ("outer"or"inner")- Tick direction. The default is "outer".
ticklabelorientation:str ("vertical"or"horizontal")- Tick label orientation. The default is "vertical".
Returns
None
Expand source code
def tickplot(self, garc_id, raxis_range=None, tickinterval=1000, tickpositions=None, ticklabels=None, tickwidth=1, tickcolor="#303030", ticklabelsize=10, ticklabelcolor="#303030", ticklabelmargin=10, tickdirection="outer", ticklabelorientation="vertical"): """ Plot ticks on the arc of the Garc class object Parameters ---------- garc_id : str ID of the Garc class object. The ID should be in Gcircle object.garc_dict. raxis_range : tuple (top=int, bottom=int) Radial axis range where tick plot is drawn. If direction is "inner", the default is `(r0 - 0.5 * abs(r1 -r0), r0)`. If direction is "outer", the default is `(r1, r1 + 0.5 * abs(r1 -r0))`. `r0, r1 = Garc_object.raxis_range[0], Garc_object.raxis_range[1]` tickinterval : int Tick interval. The default is 1000. If `tickpositions` value is given, this value will be ignored. tickpositions : list of int Positions on the arc of the Garc class object. If you set ticks on your specified positions, please use this parameter instead of tickinterval The values should be less than `Garc_object.size`. ticklabels : list of int or list or str Labels for ticks on the arc of the Garc class object. The default is same with tickpositions. tickwidth : float Tick width. The default is 1.0. tickcolor : str or float representing color code Tick color. The default is "#303030" ticklabelsize : float Tick label fontsize. The default is 10. ticklabelcolor : str Tick label color, The default is "#303030". ticklabelmargin : float Tick label margin. The default is 10. tickdirection : str ("outer" or "inner") Tick direction. The default is "outer". ticklabelorientation : str ("vertical" or "horizontal") Tick label orientation. The default is "vertical". Returns ------- None """ start = self._garc_dict[garc_id].coordinates[0] end = self._garc_dict[garc_id].coordinates[-1] size = self._garc_dict[garc_id].size + 1 positions_all = np.linspace(start, end, size, endpoint=True) if raxis_range is None: r0, r1 = self._garc_dict[garc_id].raxis_range tickheight = 0.5 * abs(r1 - r0) if tickdirection == "outer": raxis_range = (r1, r1 + tickheight) elif tickdirection == "inner": raxis_range = (r0 - tickheight, r0) if tickpositions is None: tickpositions = [pos for pos in range(0, size, tickinterval)] if ticklabels is None: ticklabels = [None] * len(tickpositions) elif ticklabels == "None": ticklabels = tickpositions for pos, label in zip(tickpositions, ticklabels): self.ax.plot([positions_all[pos], positions_all[pos]], raxis_range, linewidth=tickwidth, color=tickcolor) if label is None: pass else: ticklabel_rot = self._get_label_rotation(start + ((end - start) * (pos / size)), ticklabelorientation) if ticklabelorientation == "horizontal": label_width = ticklabelsize * 2 elif ticklabelorientation == "vertical": label_width = ticklabelsize * len(str(label)) if tickdirection == "outer": y_pos = raxis_range[1] + (label_width + ticklabelmargin) elif tickdirection == "inner": y_pos = raxis_range[0] - (label_width + ticklabelmargin) self.ax.text(positions_all[pos], y_pos, str(label), rotation=ticklabel_rot, ha="center", va="center", fontsize=ticklabelsize, color=ticklabelcolor) def save(self, file_name='test', format='pdf', dpi=None)-
Save image of Gcircle class figure object
Parameters
file_name:str, optional- File name of figure. The default is "test".
format:str, optional- File format of figure. The default is "pdf"
dpi:int, optional- Dpi of figure. The default is None.
Returns
None
Expand source code
def save(self, file_name="test", format="pdf", dpi=None): """ Save image of Gcircle class figure object Parameters ---------- file_name : str, optional File name of figure. The default is "test". format : str, optional File format of figure. The default is "pdf" dpi : int, optional Dpi of figure. The default is None. Returns ------- None """ self.figure.patch.set_alpha(0.0) if format == "pdf" and dpi is None: self.figure.savefig(file_name + ".pdf", bbox_inches="tight") else: if dpi is None: dpi = 600 self.figure.savefig(file_name + "." + format, bbox_inches="tight", dpi=dpi) return self.figure