Mercurial > repos > bgruening > deeptools_plot_correlation

comparison plotCorrelation.xml @ 8:a48149b2cb5e draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
author bgruening
date Wed, 23 Dec 2015 14:41:43 -0500
parents 44d87fb8403e
children 59ca699c7b77
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7:44d87fb8403e 8:a48149b2cb5e
90 <![CDATA[ 90 <![CDATA[
91 **What it does** 91 **What it does**
92 92
93 This tools takes a compressed matrix of scores (such as read coverages) for a number of genomic regions 93 This tools takes a compressed matrix of scores (such as read coverages) for a number of genomic regions
94 and different samples. It can visualize the correlation among samples as scatterplots or as 94 and different samples. It can visualize the correlation among samples as scatterplots or as
95 heatmap of correlation coefficients. Further output files are optional. 95 a heatmap of correlation coefficients. Further output files are optional.
96 The compressed input matrices are easily generated using the "bamCorrelate" and "bigwigCorrelate" modules of deeptools. 96 The compressed input matrices are easily generated using the "bamCorrelate" and "bigwigCorrelate" tools.
97 97
98 98
99 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png 99 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
100 :alt: Heatmap of RNA Polymerase II ChIP-seq 100 :alt: Heatmap of RNA Polymerase II ChIP-seq
101 101
109 see below for an example 109 see below for an example
110 - data matrix (optional): if you want to analyze or plot the correlation values using a different program, e.g. R, this matrix can be used 110 - data matrix (optional): if you want to analyze or plot the correlation values using a different program, e.g. R, this matrix can be used
111 111
112 **Output with test dataset**: 112 **Output with test dataset**:
113 113
114 Following is the output of plotCorrelation with our test ChIP-Seq datasets. Average coverages were computed over 10kb bins for chromosome X, 114 The following is the output of plotCorrelation with our test ChIP-Seq datasets. Average coverages were computed over 10kb bins for chromosome X,
115 from bigwig files using bigwigCorrelate. The output was used by plotCorrelation to make a heatmap of spearman correlation between samples. 115 from bigwig files using bigwigCorrelate. The output was used by plotCorrelation to make a heatmap of spearman correlation between samples.
116 116
117 .. image:: $PATH_TO_IMAGES/plotCorrelation_galaxy_bw_heatmap_output.png 117 .. image:: $PATH_TO_IMAGES/plotCorrelation_galaxy_bw_heatmap_output.png
118 118
119 119