Mercurial > repos > bgruening > deeptools_plot_correlation
changeset 16:7c0b9268fbb9 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
| author | bgruening |
|---|---|
| date | Wed, 09 Mar 2016 17:28:06 -0500 |
| parents | 714250469582 |
| children | 1d9b752e9577 |
| files | deepTools_macros.xml plotCorrelation.xml test-data/bamCoverage_result5.bw test-data/computeMatrix_result1.gz test-data/computeMatrix_result2.gz test-data/computeMatrix_result3.gz test-data/heatmapper_result1.png test-data/heatmapper_result2.png test-data/heatmapper_result2.tabular test-data/plotCorrelation_result1.png test-data/plotCoverage_result1.png test-data/plotPCA_result1.png test-data/plotPCA_result2.png test-data/plotPCA_result2.tabular test-data/profiler_result1.png test-data/profiler_result2.png test-data/profiler_result2.tabular |
| diffstat | 17 files changed, 27 insertions(+), 19 deletions(-) [+] |
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--- a/deepTools_macros.xml Thu Feb 18 11:35:58 2016 -0500 +++ b/deepTools_macros.xml Wed Mar 09 17:28:06 2016 -0500 @@ -72,12 +72,12 @@ </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.1.0</token> + <token name="@WRAPPER_VERSION@">2.2.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> <requirement type="binary">@BINARY@</requirement> - <requirement type="package" version="2.1.0">deepTools</requirement> + <requirement type="package" version="2.2.2">deepTools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -310,13 +310,13 @@ <xml name="multiple_input_bams"> <param argument="--bamfiles" type="data" format="bam" min="1" label="Bam file" multiple="true" - help="The BAM file must be sorted."/> + help=""/> </xml> <xml name="multiple_input_bams_min2"> <param argument="--bamfiles" type="data" format="bam" min="2" label="Bam file" multiple="true" - help="The BAM file must be sorted."/> + help=""/> </xml> <xml name="multiple_input_bigwigs">
--- a/plotCorrelation.xml Thu Feb 18 11:35:58 2016 -0500 +++ b/plotCorrelation.xml Wed Mar 09 17:28:06 2016 -0500 @@ -75,7 +75,7 @@ <param name="outFileFormat" value="png" /> <param name="outFileCorMatrix" value="True" /> <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" /> - <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="200" /> + <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="300" /> </test> <test> <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" /> @@ -83,20 +83,19 @@ <param name="whatToPlot" value="scatterplot" /> <param name="removeOutliers" value="True" /> <param name="plotTitle" value="Test Plot" /> - <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="200" /> + <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="300" /> </test> </tests> <help> <![CDATA[ What it does --------------- +------------ This tools takes the default output of ``multiBamSummary`` or ``multiBigwigSummary``, and computes the pairwise correlation among samples. -Results can be visualized as **scatterplots** or as -a **heatmap** of correlation coefficients (see below for examples). +Results can be visualized as **scatterplots** or as a **heatmap** of correlation coefficients (see below for examples). -Background ------------- +Theoretical Background +---------------------- The result of the correlation computation is a **table of correlation coefficients** that indicates how "strong" the relationship between two samples is and it will consist of numbers between -1 and 1. (-1 indicates perfect anti-correlation, 1 perfect correlation.) @@ -106,18 +105,18 @@ The *Spearman method* is based on **rankings**. Output --------- +------ The default output is a **diagnostic plot** -- either a scatterplot or a clustered heatmap displaying the values for each pair-wise correlation (see below for example plots). Optionally, you can also obtain a table of the pairwise correlation coefficients. .. image:: $PATH_TO_IMAGES/plotCorrelation_output.png - :width: 600 - :height: 271 + :width: 600 + :height: 271 Example plots --------------- +------------- The following is the output of ``plotCorrelation`` with our test ChIP-Seq datasets (to be found under "Shared Data" --> "Data Library"). @@ -125,14 +124,14 @@ from bigWig files using ``multiBigwigSummary``. This was then used with ``plotCorrelation`` to make a heatmap of Spearman correlation coefficients. .. image:: $PATH_TO_IMAGES/plotCorrelation_galaxy_bw_heatmap_output.png - :width: 600 - :height: 518 + :width: 600 + :height: 518 The scatterplot could look like this: .. image:: $PATH_TO_IMAGES/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png - :width: 600 - :height: 600 + :width: 600 + :height: 600 -----
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmapper_result2.tabular Wed Mar 09 17:28:06 2016 -0500 @@ -0,0 +1,3 @@ +bin labels -0.0Kb 0.0Kb +bins 1 2 +file_0 genes 2477942.34473 2610259.65234