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Plot profile color map #971

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merged 5 commits into from
Jul 23, 2020
Merged

Plot profile color map #971

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d365371
Now colors can be set by user for any heatmap in plotProfile. A bug i…
Jul 13, 2020
c08fbb5
added a small description
Jul 13, 2020
2ae9fbf
Merge remote-tracking branch 'origin/develop' into plotProfile_colorMap
Jul 23, 2020
636b750
Merge remote-tracking branch 'origin/develop' into plotProfile_colorMap
Jul 23, 2020
a3c133b
pep8 fix
Jul 23, 2020
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17 changes: 12 additions & 5 deletions deeptools/plotProfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

import argparse
import numpy as np
from math import ceil
import matplotlib
matplotlib.use('Agg')
matplotlib.rcParams['pdf.fonttype'] = 42
Expand Down Expand Up @@ -458,6 +459,13 @@ def plotly_hexbin(self):
py.plot(fig, filename=self.out_file_name, auto_open=False)

def plot_heatmap(self):
cmap = ['RdYlBu_r']
if self.color_list is not None: # check the length to be equal to the numebr of plots otherwise multiply it!
cmap = self.color_list
if len(cmap) < self.numplots:
all_colors = cmap
for i in range(ceil(self.numplots / len(cmap))):
cmap.extend(all_colors)
matrix_flatten = None
if self.y_min == [None]:
matrix_flatten = self.hm.matrix.flatten()
Expand All @@ -479,7 +487,6 @@ def plot_heatmap(self):

ax_list = []
# turn off y ticks

for plot in range(self.numplots):
labels = []
col = plot % self.plots_per_row
Expand All @@ -503,9 +510,10 @@ def plot_heatmap(self):

if self.per_group:
title = self.hm.matrix.group_labels[plot]
tickIdx = plot % self.hm.matrix.get_num_samples()
else:
title = self.hm.matrix.sample_labels[plot]

tickIdx = plot
ax.set_title(title)
mat = [] # when drawing a heatmap (in contrast to drawing lines)
for data_idx in range(self.numlines):
Expand All @@ -526,13 +534,12 @@ def plot_heatmap(self):
label = sub_matrix['group']
labels.append(label)
mat.append(np.ma.__getattribute__(self.averagetype)(sub_matrix['matrix'], axis=0))

img = ax.imshow(np.vstack(mat), interpolation='nearest',
cmap='RdYlBu_r', aspect='auto', vmin=localYMin, vmax=localYMax)
cmap=cmap[plot], aspect='auto', vmin=localYMin, vmax=localYMax)
self.fig.colorbar(img, cax=cax)

totalWidth = np.vstack(mat).shape[1]
xticks, xtickslabel = self.getTicks(plot)
xticks, xtickslabel = self.getTicks(tickIdx)
if np.ceil(max(xticks)) != float(totalWidth - 1):
tickscale = float(totalWidth) / max(xticks)
xticks_use = [x * tickscale for x in xticks]
Expand Down