Thanks to visit codestin.com
Credit goes to github.com

Skip to content

[WIP] added auto to plotheatmap #908 #982

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
LeilyR merged 4 commits into from
Aug 10, 2020
Merged

[WIP] added auto to plotheatmap #908 #982

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
5e13340
added auto to plotheatmap
Aug 7, 2020
f37e5a8
fixed lint, added warning message, updated the help for zmin, zmax
Aug 10, 2020
61ecdcd
galaxy test plotPCA
Aug 10, 2020
7a67ee3
lower down the delat for potPCA galaxy test
Aug 10, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 6 additions & 4 deletions deeptools/parserCommon.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -704,15 +704,17 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):
default=None,
help='Minimum value for the heatmap intensities. Multiple values, separated by '
'spaces can be set for each heatmap. If the number of zMin values is smaller than'
'the number of heatmaps the values are recycled.',
type=float,
'the number of heatmaps the values are recycled. If a value is set to "auto", it will be set '
' to the first percentile of the matrix values.',
type=str,
nargs='+')
optional.add_argument('--zMax', '-max',
default=None,
help='Maximum value for the heatmap intensities. Multiple values, separated by '
'spaces can be set for each heatmap. If the number of zMax values is smaller than'
'the number of heatmaps the values are recycled.',
type=float,
'the number of heatmaps the values are recycled. If a value is set to "auto", it will be set '
' to the 98th percentile of the matrix values.',
type=str,
nargs='+')
optional.add_argument('--heatmapHeight',
help='Plot height in cm. The default for the heatmap '
Expand Down
27 changes: 27 additions & 0 deletions deeptools/plotHeatmap.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -412,6 +412,16 @@ def plotMatrix(hm, outFileName,
zMin = [None]
else:
zMin = [zMin] # convert to list to support multiple entries
elif 'auto' in zMin:
matrix_flatten = hm.matrix.flatten()
auto_min = np.percentile(matrix_flatten, 1.0)
if np.isnan(auto_min):
auto_min = None
new_mins = [float(x) if x != 'auto' else auto_min for x in zMin]
zMin = new_mins
else:
new_mins = [float(x) for x in zMin]
zMin = new_mins

if zMax is None:
if matrix_flatten is None:
Expand All @@ -422,6 +432,23 @@ def plotMatrix(hm, outFileName,
zMax = [None]
else:
zMax = [zMax]
elif 'auto' in zMax:
matrix_flatten = hm.matrix.flatten()
auto_max = np.percentile(matrix_flatten, 98.0)
if np.isnan(auto_max):
auto_max = None
new_maxs = [float(x) if x != 'auto' else auto_max for x in zMax]
zMax = new_maxs
else:
new_maxs = [float(x) for x in zMax]
zMax = new_maxs
if (len(zMin) > 1) & (len(zMax) > 1):
for index, value in enumerate(zMax):
if value <= zMin[index]:
sys.stderr.write("Warnirng: In bigwig {}, the given zmin ({}) is larger than "
"or equal to the given zmax ({}). Thus, it has been set "
"to None. \n".format(index + 1, zMin[index], value))
zMin[index] = None

if yMin is None:
yMin = [None]
Expand Down
2 changes: 1 addition & 1 deletion galaxy/wrapper/plotPCA.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@
<param name="outFileFormat" value="png" />
<param name="outFileNameData" value="True" />
<output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" />
<output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" />
<output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" compare="sim_size" delta="12000" />
</test>
</tests>
<help>
Expand Down