dpryan79
commented
8 years ago Hi Marc,
The --zMin and --zMax options largely do this already.
Regarding sorting, yes it uses all samples in each group at once, otherwise the samples wouldn't get sorted together and the resulting plot would be difficult to interpret.
Devon
Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany devon.ryan@dzne.de
On Fri, May 13, 2016 at 8:45 AM, Marc notifications@github.com wrote:
I think that it would be nice to have the "--minThreshold" and "--maxThreshold" arguments in plotHeatmap as well. computeMatrix with multiple samples can take quite a long time and being able to set the thresholds only during plotting would help to find a senseful value quicker (to kick out abnormal regions).
Note aside - I assume that the sorting in plotHeatmap uses all data/samples for a given region at once, but somehow it isn't entirely clear to me from the documentation whether this is true (the alternative would be that each sample is sorted separately - meaning that one line along the plot does not reflect one region, but many).
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MWSchmid
I think that it would be nice to have the "--minThreshold" and "--maxThreshold" arguments in plotHeatmap as well. computeMatrix with multiple samples can take quite a long time and being able to set the thresholds only during plotting would help to find a senseful value quicker (to kick out abnormal regions).
Note aside - I assume that the sorting in plotHeatmap uses all data/samples for a given region at once, but somehow it isn't entirely clear to me from the documentation whether this is true (the alternative would be that each sample is sorted separately - meaning that one line along the plot does not reflect one region, but many).