Mercurial > repos > bgruening > deeptools_plot_correlation

comparison plotCorrelation.xml @ 3:df65a17fb5d1 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
author bgruening
date Wed, 09 Mar 2016 18:20:03 -0500
parents fcb4e6e95544
children cdde99ce71c8
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2:fcb4e6e95544 3:df65a17fb5d1
73 <test> 73 <test>
74 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" /> 74 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
75 <param name="outFileFormat" value="png" /> 75 <param name="outFileFormat" value="png" />
76 <param name="outFileCorMatrix" value="True" /> 76 <param name="outFileCorMatrix" value="True" />
77 <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" /> 77 <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
78 <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="200" /> 78 <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="300" />
79 </test> 79 </test>
80 <test> 80 <test>
81 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" /> 81 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
82 <param name="outFileFormat" value="png" /> 82 <param name="outFileFormat" value="png" />
83 <param name="whatToPlot" value="scatterplot" /> 83 <param name="whatToPlot" value="scatterplot" />
84 <param name="removeOutliers" value="True" /> 84 <param name="removeOutliers" value="True" />
85 <param name="plotTitle" value="Test Plot" /> 85 <param name="plotTitle" value="Test Plot" />
86 <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="200" /> 86 <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="300" />
87 </test> 87 </test>
88 </tests> 88 </tests>
89 <help> 89 <help>
90 <![CDATA[ 90 <![CDATA[
91 What it does 91 What it does
92 -------------- 92 ------------
93 93
94 This tools takes the default output of ``multiBamSummary`` or ``multiBigwigSummary``, and computes the pairwise correlation among samples. 94 This tools takes the default output of ``multiBamSummary`` or ``multiBigwigSummary``, and computes the pairwise correlation among samples.
95 Results can be visualized as **scatterplots** or as 95 Results can be visualized as **scatterplots** or as a **heatmap** of correlation coefficients (see below for examples).
96 a **heatmap** of correlation coefficients (see below for examples).
97 96
98 Background 97 Theoretical Background
99 ------------ 98 ----------------------
100 99
101 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.) 100 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.)
102 101
103 We offer two different functions for the correlation computation: *Pearson* or *Spearman*. 102 We offer two different functions for the correlation computation: *Pearson* or *Spearman*.
104 103
105 The *Pearson method* measures the **metric differences** between samples and is therefore influenced by outliers. 104 The *Pearson method* measures the **metric differences** between samples and is therefore influenced by outliers.
106 The *Spearman method* is based on **rankings**. 105 The *Spearman method* is based on **rankings**.
107 106
108 Output 107 Output
109 -------- 108 ------
110 109
111 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). 110 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).
112 111
113 Optionally, you can also obtain a table of the pairwise correlation coefficients. 112 Optionally, you can also obtain a table of the pairwise correlation coefficients.
114 113
115 .. image:: $PATH_TO_IMAGES/plotCorrelation_output.png 114 .. image:: $PATH_TO_IMAGES/plotCorrelation_output.png
116 :width: 600 115 :width: 600
117 :height: 271 116 :height: 271
118 117
119 Example plots 118 Example plots
120 -------------- 119 -------------
121 120
122 The following is the output of ``plotCorrelation`` with our test ChIP-Seq datasets (to be found under "Shared Data" --> "Data Library"). 121 The following is the output of ``plotCorrelation`` with our test ChIP-Seq datasets (to be found under "Shared Data" --> "Data Library").
123 122
124 Average coverages were computed over 10 kb bins for chromosome X, 123 Average coverages were computed over 10 kb bins for chromosome X,
125 from bigWig files using ``multiBigwigSummary``. This was then used with ``plotCorrelation`` to make a heatmap of Spearman correlation coefficients. 124 from bigWig files using ``multiBigwigSummary``. This was then used with ``plotCorrelation`` to make a heatmap of Spearman correlation coefficients.
126 125
127 .. image:: $PATH_TO_IMAGES/plotCorrelation_galaxy_bw_heatmap_output.png 126 .. image:: $PATH_TO_IMAGES/plotCorrelation_galaxy_bw_heatmap_output.png
128 :width: 600 127 :width: 600
129 :height: 518 128 :height: 518
130 129
131 The scatterplot could look like this: 130 The scatterplot could look like this:
132 131
133 .. image:: $PATH_TO_IMAGES/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png 132 .. image:: $PATH_TO_IMAGES/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png
134 :width: 600 133 :width: 600
135 :height: 600 134 :height: 600
136 135
137 ----- 136 -----
138 137
139 @REFERENCES@ 138 @REFERENCES@
140 ]]> 139 ]]>