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return proper numpy NANs in plotFingerprint.py (instead of "NA" strings) #999

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return proper numpy NANs in plotFingerprint.py (instead of "NA" strings) #999

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6e6903b
Fixes for 3.4.2
dpryan79 Apr 4, 2020
61e3b1b
disable azure on OSX
dpryan79 Apr 4, 2020
53e2b47
Merge branch 'develop' of https://github.com/deeptools/deepTools into…
dpryan79 May 2, 2020
4517fb6
Closes #945
dpryan79 May 2, 2020
80b1d60
computeMatricOperation dataRange (#951)
LeilyR Jul 23, 2020
705f36d
fixed a little typo in bamCompare (#967)
LeilyR Jul 23, 2020
1d0c0ce
save the output matrix of the plotheatmap in a format to be compatibl…
LeilyR Jul 23, 2020
a3ddfd4
Plot profile color map (#971)
LeilyR Jul 23, 2020
86e46d0
added sortUsingSamples and clusterUsingSamples to the galaxy wrapper
Jul 23, 2020
979241f
[WIP] added auto to plotheatmap #908 (#982)
LeilyR Aug 10, 2020
6dee0c3
Merge branch 'fix_976' of https://github.com/deeptools/deepTools into…
Aug 10, 2020
b1e1d20
fix #969 (#970)
dpryan79 Aug 10, 2020
e3720eb
fixed plotHeatmap.xml by removing size from the the params and adding…
Aug 10, 2020
4b4c33f
Merge remote-tracking branch 'origin/develop' into fix_976
Aug 10, 2020
f36326a
upated change.txt
Aug 10, 2020
83649ed
updated the doc html
Aug 11, 2020
f773fdf
Merge pull request #977 from deeptools/fix_976
bgruening Aug 21, 2020
920ab59
return proper numpy s in plotFingerprint.py (instead of strings)
dlaehnemann Sep 16, 2020
ee70996
add usegalaxy.eu badge
bgruening Aug 21, 2020
d8dec04
return proper numpy s in plotFingerprint.py (instead of strings)
dlaehnemann Sep 16, 2020
f4ec71b
Merge branch 'plot-fingerprint_return-proper-NANs' of https://github.…
dlaehnemann Sep 17, 2020
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10 changes: 5 additions & 5 deletions deeptools/plotFingerprint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -202,10 +202,10 @@ def getCHANCE(args, idx, mat):
"""
# Get the index of the reference sample
if args.JSDsample not in args.bamfiles:
return ["NA", "NA", "NA"]
return [np.NAN, np.NAN, np.NAN]
refIdx = args.bamfiles.index(args.JSDsample)
if refIdx == idx:
return ["NA", "NA", "NA"]
return [np.NAN, np.NAN, np.NAN]

subMatrix = np.copy(mat[:, [idx, refIdx]])
subMatrix[np.isnan(subMatrix)] = 0
Expand Down Expand Up @@ -271,10 +271,10 @@ def getJSD(args, idx, mat):

# Get the index of the reference sample
if args.JSDsample not in args.bamfiles:
return "NA"
return np.NAN
refIdx = args.bamfiles.index(args.JSDsample)
if refIdx == idx:
return "NA"
return np.NAN

# These will hold the coverage histograms
chip = np.zeros(MAXLEN, dtype=np.int)
Expand Down Expand Up @@ -338,7 +338,7 @@ def signalAndBinDist(x):

if abs(sum(PMFinput) - 1) > 0.01 or abs(sum(PMFchip) - 1) > 0.01:
sys.stderr.write("Warning: At least one PMF integral is significantly different from 1! The JSD will not be returned")
return "NA"
return np.NAN

# Compute the JSD from the PMFs
M = (PMFinput + PMFchip) / 2.0
Expand Down