目的是创造一个情节。我有以下脚本:
#!/usr/bin/python
import sys
from matplotlib import pyplot as plt
from matplotlib.collections import BrokenBarHCollection
file = sys.argv[1]
color_lookup = {
'INS': (1., 1., 1.),
'DEL': (.6, .6, .6),
'DUP': (.4, .4, .4),
'INV': (.2, .2, .2),
'TRA': (0., 0., 0.),
}
height = 0.9
spacing = 0.9
def ideograms(fn):
last_chrom = None
fin = open(fn)
fin.readline()
xranges, colors = [], []
ymin = 0
print "Reading input..."
for line in fin:
chrom, start, stop, label = line.strip().split('\t')
start = int(start)
stop = int(stop)
width = stop - start
if chrom == last_chrom or (last_chrom is None):
xranges.append((start, width))
colors.append(color_lookup[label])
last_chrom = chrom
continue
ymin += height + spacing
yrange = (ymin, height)
yield xranges, yrange, colors, last_chrom
xranges, colors = [], []
xranges.append((start, width))
colors.append(color_lookup[label])
last_chrom = chrom
# last one
ymin += height + spacing
yrange = (ymin, height)
yield xranges, yrange, colors, last_chrom
fig = plt.figure()
ax = fig.add_subplot(111)
d = {}
yticks = []
yticklabels = []
# ideogram.txt downloaded from UCSC's table browser
for xranges, yrange, colors, label in ideograms(file):
coll = BrokenBarHCollection(xranges, yrange, facecolors=colors)
ax.add_collection(coll)
center = yrange[0] + yrange[1]/2.
yticks.append(center)
yticklabels.append(label)
d[label] = xranges
ax.axis('tight')
ax.set_yticks(yticks)
ax.set_yticklabels(yticklabels)
ax.set_xticks([])
fig.show()
它接受以下文本文件:
^{pr2}$但脚本不输出任何绘图,也不会给出任何错误。你知道发生了什么事吗?在
编辑:我刚刚删除了center = yrange[0] + yrange[1]/2.
之后的那一点,现在它抛出以下错误/home/software/002-Interpreters/lib/python2.7/site-packages/matplotlib/figure.py:387: UserWarning: matplotlib is currently using a non-GUI backend, so cannot show the figure
"matplotlib is currently using a non-GUI backend, "
。在
目前没有回答
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