Mercurial > repos > bgruening > deeptools_plot_heatmap
diff plotHeatmap.xml @ 7:aaf01404686f draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41
| author | bgruening |
|---|---|
| date | Wed, 23 Dec 2015 03:54:30 -0500 |
| parents | 59f925c67e2f |
| children | 8ed7e3b6a16c |
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--- a/plotHeatmap.xml Tue Dec 22 13:41:44 2015 -0500 +++ b/plotHeatmap.xml Wed Dec 23 03:54:30 2015 -0500 @@ -32,7 +32,7 @@ #if $advancedOpt.sortRegions: --sortRegions '$advancedOpt.sortRegions' #end if - + #if $advancedOpt.sortUsing: --sortUsing '$advancedOpt.sortUsing' #end if @@ -69,7 +69,7 @@ --whatToShow '$advancedOpt.whatToShow' - --startLabel '$advancedOpt.startLabel' + --startLabel '$advancedOpt.startLabel' --endLabel '$advancedOpt.endLabel' --refPointLabel '$advancedOpt.referencePointLabel' --regionsLabel '$advancedOpt.regionsLabel' @@ -78,7 +78,7 @@ --plotTitle '$advancedOpt.plotTitle' #end if - $advancedOpt.perGroup + $advancedOpt.onePlotPerGroup @KMEANS_CLUSTERING@ @@ -113,7 +113,7 @@ <option value="std">std</option> </param> - <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color" + <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color" help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. @@ -143,7 +143,9 @@ help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar."> <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option> <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option> + <option value="heatmap only">heatmap only</option> <option value="heatmap and colorbar">heatmap and colorbar</option> + <option value="colorbar only">colorbar only</option> </param> <param argument="--startLabel" type="text" value="TSS" size="10" @@ -156,8 +158,8 @@ <param argument="--referencePointLabel" type="text" value="TSS" size="10" label="Reference point label" help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. "peak start" etc." /> - <param argument="--regionsLabel" type="text" value="genes" size="30" - label="Labels for the regions plotted in the heatmap" + <param argument="--regionsLabel" type="text" value="genes" size="30" + label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2."> <sanitizer> <valid initial="string.printable"> @@ -165,12 +167,10 @@ </sanitizer> </param> <expand macro="plotTitle" /> - <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" - label="Do one plot per group" - help="When clustering is applied to the data, or the computematrix was performed on file containing - groups separated by "#", plot the groups next to each other. The default is to plot - the samples next to each other. If this option is set, each group (or cluster) will get its own plot, - with different samples stacked on top of each other."/> + <param argument="--onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" + label="Do one plot per group" + help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. + If this option is set, each group will get its own plot, stacked on top of each other."/> <expand macro="kmeans_clustering" /> </when> @@ -199,17 +199,19 @@ The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. Like profiler, it requires that computeMatrix was run first to calculate the values. + +We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as +with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of +groups with similar read distributions that you expect and the algorithm will do the sorting for you. -We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values -displayed in the heatmap as well as with the different coloring options. The most powerful option is the k-means/hirarchichal clustering -where you simply need to indicate the number of groups with similar read distributions that you expect and the algorithm will do the sorting for you. +Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png :alt: Heatmap of RNA Polymerase II ChIP-seq -You can find more details on the tool on the plotHeatmap doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotHeatmap.html +You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper -----