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Adding independent ranges by sample option: for zMax zMin yMin and y… #1116

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Adding independent ranges by sample option: for zMax zMin yMin and y… #1116

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Adding independent ranges by sample option: for zMax zMin yMin and y…
Jan 20, 2022
a9ebb1e
small style changes
bgruening Apr 4, 2023
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8 changes: 8 additions & 0 deletions deeptools/heatmapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1150,6 +1150,14 @@ def get_num_samples(self):
def get_num_groups(self):
return len(self.group_labels)

def get_percentile_by_samples(self, percentile):
percentile_per_samples = []
for sample in range(self.get_num_samples()):
sample_start = self.sample_boundaries[sample]
sample_end = self.sample_boundaries[sample + 1]
percentile_per_samples.append(np.percentile(np.ma.masked_invalid(self.matrix[:,sample_start:sample_end]),percentile))
return percentile_per_samples

def set_group_labels(self, new_labels):
""" sets new labels for groups
"""
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13 changes: 13 additions & 0 deletions deeptools/plotHeatmap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,11 @@ def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType
# It turns out that set_ylim only takes np.float64s
for sample_id, subplot in enumerate(ax_list):
localYMin = yMin[sample_id % len(yMin)]
if localYMin == "independent":
localYMin = ax_list[sample_id].get_ylim()[0]
localYMax = yMax[sample_id % len(yMax)]
if localYMax == "independent":
localYMax = ax_list[sample_id].get_ylim()[1]
lims = [globalYmin, globalYmax]
if localYMin:
if localYMax:
Expand Down Expand Up @@ -412,6 +416,8 @@ def plotMatrix(hm, outFileName,
zMin = [None]
else:
zMin = [zMin] # convert to list to support multiple entries
elif zMin == ["independent"]:
zMin = hm.matrix.get_percentile_by_samples(1.0)
elif 'auto' in zMin:
matrix_flatten = hm.matrix.flatten()
auto_min = np.percentile(matrix_flatten, 1.0)
Expand All @@ -432,6 +438,8 @@ def plotMatrix(hm, outFileName,
zMax = [None]
else:
zMax = [zMax]
elif zMax == ["independent"]:
zMax = hm.matrix.get_percentile_by_samples(98.0)
elif 'auto' in zMax:
matrix_flatten = hm.matrix.flatten()
auto_max = np.percentile(matrix_flatten, 98.0)
Expand All @@ -452,8 +460,13 @@ def plotMatrix(hm, outFileName,

if yMin is None:
yMin = [None]
elif yMin == ["independent"]:
yMin = ["independent"] * hm.matrix.get_num_samples()

if yMax is None:
yMax = [None]
elif yMax == ["independent"]:
yMax = ["independent"] * hm.matrix.get_num_samples()
if not isinstance(yMin, list):
yMin = [yMin]
if not isinstance(yMax, list):
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