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Added sortUsingSamples and clusterUsingSamples to the galaxy wrapper #977

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Merged
bgruening merged 6 commits into from
Aug 21, 2020
Merged

Added sortUsingSamples and clusterUsingSamples to the galaxy wrapper #977

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86e46d0
added sortUsingSamples and clusterUsingSamples to the galaxy wrapper
Jul 23, 2020
6dee0c3
Merge branch 'fix_976' of https://github.com/deeptools/deepTools into…
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
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3 changes: 2 additions & 1 deletion CHANGES.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,8 @@
* Fixed a small typo in bamCompare. (issue #966)
* Save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again.(issue #953)
* Different colors can now be set by user for plotProfile --plotType heatmap (issue #956)
* `auto` option now has been added to the zMin and zMax of plotHeatmap. (issue #908)
* Added the `auto` option to the zMin and zMax of plotHeatmap. (issue #908)
* Added `--sortUsingSamples` and `--clusterUsingSamples` to the plotHeatmap galaxy wrapper. (issue #976)

3.4.3

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6 changes: 3 additions & 3 deletions deeptools/parserCommon.py
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Expand Up @@ -613,9 +613,9 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):

optional.add_argument('--sortUsingSamples',
help='List of sample numbers (order as in matrix), '
'that are used for sorting by --sortUsing, '
'no value uses all samples, '
'example: --sortUsingSamples 1 3',
'which are used by --sortUsing for sorting. '
'If no value is set, it uses all samples. '
'Example: --sortUsingSamples 1 3',
type=int, nargs='+')

optional.add_argument('--linesAtTickMarks',
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46 changes: 35 additions & 11 deletions galaxy/wrapper/plotHeatmap.xml
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Expand Up @@ -75,9 +75,15 @@
#if str($advancedOpt.yMin).strip() != "":
--yMin $advancedOpt.yMin
#end if
#if $advancedOpt.yMax:
#if str($advancedOpt.yMax).strip() != "":
--yMax $advancedOpt.yMax
#end if
#if str($advancedOpt.sortUsingSamples).strip() != "":
--sortUsingSamples $advancedOpt.sortUsingSamples
#end if
#if str($advancedOpt.clusterUsingSamples).strip() != "":
--clusterUsingSamples $advancedOpt.clusterUsingSamples
#end if

--xAxisLabel '$advancedOpt.xAxisLabel'
--yAxisLabel '$advancedOpt.yAxisLabel'
Expand Down Expand Up @@ -134,6 +140,15 @@
<when value="yes">
<expand macro="sortRegions" />
<expand macro="sortUsing" />
<param argument="--sortUsingSamples" type="text"
label="List of samples to be used for sorting"
help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting.
If no value is set, it uses all samples. Example: 1 3 (space separated!)" />
<sanitizer>
<valid initial="string.printable">
<add value=" "/>
</valid>
</sanitizer>
<param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
label="Draw dashed lines in heatmap above all tick marks?" />
<param argument="--averageTypeSummaryPlot" type="select"
Expand Down Expand Up @@ -168,19 +183,19 @@
help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
be between 0 and 1. A value of 0.0 would be fully transparent." />

<param argument="--colorList" type="text" value="" size="50" optional="True"
<param argument="--colorList" type="text" value="" optional="True"
label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"
help="The color of the heatmaps can be specified as a list of colors separated by comas with
not space in between. For example: white,blue white,green will set a color map from white
to blue for the first heatmap and for white to green for the next heatmap."/>
<expand macro="zMin_zMax" />
<param argument="--yMin" type="float" value="" size="3" optional="True"
<param argument="--yMin" type="float" value="" optional="True"
label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
<param argument="--yMax" type="float" value="" size="3" optional="True"
<param argument="--yMax" type="float" value="" optional="True"
label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
<param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
<param argument="--xAxisLabel" type="text" value="distance from TSS (bp)"
label="The x-axis label" help="" />
<param argument="--yAxisLabel" type="text" value="genes" size="30"
<param argument="--yAxisLabel" type="text" value="genes"
label="The y-axis label for the top panel" help="" />

<param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
Expand All @@ -195,17 +210,17 @@
<option value="heatmap and colorbar">heatmap and colorbar</option>
</param>

<param argument="--startLabel" type="text" value="TSS" size="10"
<param argument="--startLabel" type="text" value="TSS"
label="Label for the region start"
help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
<param argument="--endLabel" type="text" value="TES" size="10"
<param argument="--endLabel" type="text" value="TES"
label="Label for the region end"
help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/>

<param argument="--referencePointLabel" type="text" value="TSS" size="10"
<param argument="--referencePointLabel" type="text" value="TSS"
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. &quot;peak start&quot; etc." />
<param argument="--samplesLabel" type="text" size="30"
<param argument="--samplesLabel" type="text"
label="Labels for the samples (each bigwig) plotted"
help="The default is to use the file name of the sample. The sample labels should be separated by
spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
Expand All @@ -214,7 +229,7 @@
</valid>
</sanitizer>
</param>
<param argument="--regionsLabel" type="text" size="30"
<param argument="--regionsLabel" type="text"
label="Labels for the regions plotted in the heatmap"
help="If more than one region is being plotted a list of labels separated by space is required.
If a label itself contains a space, then quotes are needed.
Expand All @@ -228,6 +243,15 @@
help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>

<expand macro="kmeans_clustering" />
<param argument="--clusterUsingSamples" type="text"
label="List of samples to be used for clustering"
help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering.
If no value is set, it uses all samples. Example: 1 3 (space separated!)"/>
<sanitizer>
<valid initial="string.printable">
<add value=" "/>
</valid>
</sanitizer>
</when>
</conditional>
</inputs>
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