Specify zMin / zMax / yMin / yMax to a single heatmap column #908
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There's no way to do that at the moment, though perhaps I can add an "auto" option. I'll leave this open as a feature request. |
LeilyR
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LeilyR
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* fix #969 * PEP8 * updated changes.txt * fixed a little bug in parseCommon.py which caused flake8 failure. * [WIP] added auto to plotheatmap #908 (#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>
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* Fixes for 3.4.2 * disable azure on OSX * Closes #945 * computeMatricOperation dataRange (#951) * 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 * fixed a little typo in bamCompare (#967) * save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again (#968) * Plot profile color map (#971) * 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 sortUsingSamples and clusterUsingSamples to the galaxy wrapper * [WIP] added auto to plotheatmap #908 (#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 * fix #969 (#970) * fix #969 * PEP8 * updated changes.txt * fixed a little bug in parseCommon.py which caused flake8 failure. * [WIP] added auto to plotheatmap #908 (#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 * updated version and changes * removed alpha from plotPCA test * removed compare="sim_size" * fixed plotHeatmap.xml by removing size from the the params and adding anitizer for the 2 new params. * upated change.txt * updated the doc html Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
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release 3.5.0 addresses this issue |
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Hey, nice idea to have this auto options for color ranges. I just tried this new 'auto' for --zMin and --zMax on various ChIP-seq libraries and found that it would more useful to my application, if that auto would determine the value ranges per individual sample instead of for a group of samples. Further, is there any plan to make it available for the --yMin and --yMax ? |
blaiseli
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Feb 17, 2021
* Fixes for 3.4.2 * disable azure on OSX * Closes deeptools#945 * computeMatricOperation dataRange (deeptools#951) * 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 * fixed a little typo in bamCompare (deeptools#967) * save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again (deeptools#968) * Plot profile color map (deeptools#971) * 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 sortUsingSamples and clusterUsingSamples to the galaxy wrapper * [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 * fix deeptools#969 (deeptools#970) * 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 * updated version and changes * removed alpha from plotPCA test * removed compare="sim_size" * fixed plotHeatmap.xml by removing size from the the params and adding anitizer for the 2 new params. * upated change.txt * updated the doc html Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
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When manually specifying the z/y Min/Max for
plotHeatmapof a matrix with multiple samples, is it possible to only apply the parameters to one of the heatmaps and continue to use the automatic limits for the rest? I don't want one value to be reused for each, but rather only on one of three samples, the third in this case. I tried giving the empty string to samples I don't want to set, but that didn't work.deeptools --version->deeptools 3.3.0python --version->Python 3.7.3plotHeatmap: error: argument --zMin/-min: invalid float value: ''My use case is in a script generating 30 sets of 3 heatmaps each, and eyeballing the limits for manual entry for the first two columns is getting old...
Also, great set of tools and thanks for it!
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