pyCircosで綺麗な円形グラフをplotする#2

1.前回#1

2.今回の内容barplot scatterplot lineplot heatmap chordplot

かけるようになるグラフ

2-1.使用するデータ

from pycircos import Gcircle,Garc
from collections import defaultdict
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt

general_data = './sample_data/example_data_chromosome_general.csv'
cytoband_data = './sample_data/example_data_chromosome_cytoband.csv'
point_data = './sample_data/example_data_point.csv'
bar_data = './sample_data/example_data_barplot.csv'
gradual_data = './sample_data/example_data_rect_gradual.csv'
link_data = './sample_data/example_data_links.csv'

general_data	cytoband_data
point_data	bar_data
gradual_data	link_data
">	">

2-2.arcの基本情報の設定

この過程はどのプロットをするときにも使用します。

circle = Gcircle(figsize=(8,8))
circle.set_garcs() #デフォルトは0°から360°
#gengeral file からGarcの設定
with open(general_data) as f:
    f.readline()
    for line in f:
        line = line.rstrip().split(',') #csvなのでこのようにすれば分割できる
        name = line[0]
        length = int(line[2])

        arc = Garc(
            arc_id=name,
            size=length, #arcの長さをlengthに設定
            interspace=2, #arcの間隔
            raxis_range=(950,1000), #arcの太さ
            labelposition=60, #labelの位置 arcの中心から60外側
            label_visible=True #labelを表示　Falseで非表示
            )
            circle.add_garc(arc) #arcを追加
circle.set_garcs() #デフォルトは0°から360°

2-3.barplot

barplotするためのデータを格納した辞書を作成

#dataを格納する辞書の作成
arcdata_dict = defaultdict(dict)
color_dict = {"gneg":"#FFFFFF00", "gpos25":"#EEEEEE", "gpos50":"#BBBBBB", "gpos75":"#777777", "gpos100":"#000000", "gvar":"#FFFFFF00", "stalk":"#C01E27", "acen":"#D82322"}

with open(cytoband_data) as cf:
    cf.readline()
    for line in cf:
        line = line.rstrip().split(',')
        name = line[0]
        start = int(line[1])-1
        width = int(line[2]) - start
        if name not in arcdata_dict:
            arcdata_dict[name]['positions'] = []
            arcdata_dict[name]['width'] = []
            arcdata_dict[name]['colors'] = []
        arcdata_dict[name]['positions'].append(start)
        arcdata_dict[name]['width'].append(width)
        arcdata_dict[name]['colors'].append(color_dict[line[4]])

最後にデータをもとにbarplotしていきます

for key in arcdata_dict:
    circle.barplot(
        garc_id = key,
        data = [1]*len(arcdata_dict[key]['positions']),#barの高さ今回はすべて同じ高さ,最大値がraxis_rangeの幅と同じになる
        width = arcdata_dict[key]['width'],#barの太さ
        raxis_range=[950,1000],#barを描画する範囲, arcの外に配置することも可能
        facecolor = arcdata_dict[key]['colors'], #barの色
        positions = arcdata_dict[key]['positions'] #それぞれのbarの位置
    )
circle.figure #描画

2-4.scatterplot

2-3のcircleにscatterplotを追加します。

values_all = []
arcdata_dict = defaultdict(dict)

with open(scatter_data) as f:
    f.readline()
    for line in f:
        line = line.rstrip().split(',')
        name = line[0]
        start = int(line[1]) -1
        end = int(line[2])
        mid = (start+end)/2
        value = float(line[3])
        values_all.append(value)
        if name not in arcdata_dict:
            arcdata_dict[name]['positions'] = []
            arcdata_dict[name]['values'] = []
        arcdata_dict[name]['positions'].append(mid)
        arcdata_dict[name]['values'].append(value)

vmin, vmax = min(values_all), max(values_all)
for key in arcdata_dict:
    circle.scatterplot(
        garc_id=key,
        data=arcdata_dict[key]['values'],
        positions=arcdata_dict[key]['positions'],
        rlim=[vmin-0.05*abs(vmin), vmax+0.05*abs(vmax)],
        raxis_range=(640,690),
        facecolor='orangered',
        spine=True #枠線の有無
    )

2-4.lineplot

for key in arcdata_dict:
    circle.lineplot(
        key,
        data=arcdata_dict[key]["values"],
        positions=arcdata_dict[key]["positions"], 
        rlim=[vmin-0.05*abs(vmin), vmax+0.05*abs(vmax)],
        raxis_range=(570,620),
        linecolor="royalblue",
        spine=False
        ) 

2-5.barplot

values_all   = [] 
arcdata_dict = defaultdict(dict)
with open(bar_data) as f:
    f.readline()
    for line in f:
        line  = line.rstrip().split(",")
        name  = line[0]     
        start = int(line[1])-1
        end   = int(line[2]) 
        width = end-start 
        if name not in arcdata_dict:
            arcdata_dict[name]["positions"] = []
            arcdata_dict[name]["widths"]    = [] 
            arcdata_dict[name]["values"]    = [] 
        arcdata_dict[name]["positions"].append(start) 
        arcdata_dict[name]["widths"].append(width)
        arcdata_dict[name]["values"].append(float(line[-1]))
        values_all.append(float(line[-1]))

vmin, vmax = min(values_all), max(values_all) 
for key in arcdata_dict:  
    circle.barplot(
        key,
        data=arcdata_dict[key]["values"],
        positions=arcdata_dict[key]["positions"], 
        width=arcdata_dict[key]["widths"],
        base_value=0.0,
        rlim=[vmin-0.05*abs(vmin), vmax+0.05*abs(vmax)],
        raxis_range=(500,550),
        facecolor="y", #yellow
        spine=True
        )

2-6.heatmap

values_all   = [] 
arcdata_dict = defaultdict(dict)
with open(gradual_data) as f:
    f.readline()
    for line in f:
        line  = line.rstrip().split(",")
        name  = line[0]     
        start = int(line[1])-1
        end   = int(line[2]) 
        width = end-start 
        if name not in arcdata_dict:
            arcdata_dict[name]["positions"] = []
            arcdata_dict[name]["widths"]    = [] 
            arcdata_dict[name]["values"]    = [] 
        arcdata_dict[name]["positions"].append(start) 
        arcdata_dict[name]["widths"].append(width)
        arcdata_dict[name]["values"].append(float(line[-1]))
        values_all.append(float(line[-1]))

vmin, vmax = min(values_all), max(values_all) 
for key in arcdata_dict:
    circle.heatmap(key,
                   data=arcdata_dict[key]["values"],
                   positions=arcdata_dict[key]["positions"], 
                   width=arcdata_dict[key]["widths"],
                   raxis_range=(430,480),
                   vmin=vmin, vmax=vmax, 
                   cmap=plt.cm.viridis
                   )

2-7 chordplot

values_all   = [] 
arcdata_dict = defaultdict(dict)
with open(link_data) as f:
    f.readline()
    for line in f:
        line  = line.rstrip().split(",")
        name1  = line[0]     
        start1 = int(line[1])-1
        end1   = int(line[2])
        name2  = line[3]     
        start2 = int(line[4])-1
        end2   = int(line[5])
        source = (name1, start1, end1, 425) #繋ぐもと
        destination = (name2, start2, end2, 425)#繋ぐ先
        circle.chord_plot(
            source,
            destination,
            facecolor=circle.garc_dict[name1].facecolor
            )