return proper numpy NANs in plotFingerprint.py (instead of "NA" strings)
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* Added dataRange to computeMatricOperation to return min,max,median and 10th and 90th percentile. * fixed pep8 * more pep8 fix * fixed test_sieve of azure tests * one more fix for test_sieve * imported pysam to test_readFiltering.py * updated hash values for test_sieve * fixed galaxy computeMatrixOperation.xml * More fixes for galaxy wrapper
…e with running plotheatmap on it again (deeptools#968)
* Now colors can be set by user for any heatmap in plotProfile. A bug in tick index for plotting heatmap is also fixed. * added a small description * pep8 fix
* added auto to plotheatmap * fixed lint, added warning message, updated the help for zmin, zmax * galaxy test plotPCA * lower down the delat for potPCA galaxy test Co-authored-by: Leily Rabbani <rabbani@pc390.ie-freiburg.mpg.de>
* fix deeptools#969 * PEP8 * updated changes.txt * fixed a little bug in parseCommon.py which caused flake8 failure. * [WIP] added auto to plotheatmap deeptools#908 (deeptools#982) * added auto to plotheatmap * fixed lint, added warning message, updated the help for zmin, zmax * galaxy test plotPCA * lower down the delat for potPCA galaxy test Co-authored-by: Leily Rabbani <rabbani@pc390.ie-freiburg.mpg.de> * updated version and changes * removed alpha from plotPCA test * removed compare="sim_size" Co-authored-by: Devon Ryan <devon.ryan@genedata.com> Co-authored-by: Leily Rabbani <rabbani@pc390.ie-freiburg.mpg.de> Co-authored-by: LeilyR <leila.rabbani@gmail.com>
… anitizer for the 2 new params.
Added sortUsingSamples and clusterUsingSamples to the galaxy wrapper
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could you please re-base your PR to the develop branch? Thanks! |
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Welcome to deepTools GitHub repository! Please check the following regarding
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This problem came up when parsing the OutputQualityMetrics txt output file downstream when it contains the
NAvalues in columns. To be exact, the conversion tofloat()in the multiqc module throws an error and leads to the respective plot being skipped. The conversion that fails is this line:https://github.com/ewels/MultiQC/blob/9760f7561a56c1295a661471d7447abd085b8020/multiqc/modules/deeptools/plotFingerprint.py#L110
According to the documentation of
float(), this should instead readnanto be parsed correctly. And this is whatprint(numpy.NAN)gives (also see numpy.NAN docs and what is used elsewhere in deeptools (a quick grep on thedeeptools/directory did not give any other results for"NA").