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comparison hicCorrelate.xml @ 8:2d8543aeeb65 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:33:56 -0400
parents 602a0c6f4bb0
children e89d515c3594
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7:602a0c6f4bb0 8:2d8543aeeb65
1 <tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Computes pairwise correlations between hic matrices data</description> 2 <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicCorrelate</token> 4 <token name="@BINARY@">hicCorrelate</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
38 <param name="method" type="select" label="Correlation method to use" argument="--method" > 38 <param name="method" type="select" label="Correlation method to use" argument="--method" >
39 <option value="spearman">Spearman</option> 39 <option value="spearman">Spearman</option>
40 <option selected="true" value="pearson">Pearson</option> 40 <option selected="true" value="pearson">Pearson</option>
41 </param> 41 </param>
42 <param name="log1p" type="boolean" argument="--log1p" truevalue="--log1p" falsevalue="" 42 <param name="log1p" type="boolean" argument="--log1p" truevalue="--log1p" falsevalue=""
43 label="Use the log1p of the matrix values" help="(--log1p)" /> 43 label="Use the log1p of the matrix values" help="If set, then the log1p of the matrix values is used.
44 This parameter has no effect for Spearman correlations
45 but changes the output of Pearson correlation and, for
46 the scatter plot, if set, the visualization of the
47 values is easier." />
44 48
45 <expand macro="use_range" /> 49 <expand macro="use_range" />
46 50
47 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0"> 51 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
48 <param name="chromosome" type="text"> 52 <param name="chromosome" type="text" label='chromosome (one per field)'>
49 <validator type="empty_field" /> 53 <validator type="empty_field" />
50 </param> 54 </param>
51 </repeat> 55 </repeat>
52 <expand macro="colormap" /> 56 <expand macro="colormap" />
53 </inputs> 57 </inputs>
91 <help><![CDATA[ 95 <help><![CDATA[
92 96
93 Matrix correlation 97 Matrix correlation
94 ================== 98 ==================
95 99
96 Computes pairwise correlations between Hi-C contact matrices. 100 **hicCorrelate** is a dedicated Quality Control tool that allows the correlation of multiple Hi-C matrices at once with either a heatmap or scatterplots output.
97 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.
98 101
99 Input 102 Computes pairwise correlations between Hi-C matrices data. The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices. Parameters that strongly affect correlations are bin size of the Hi-C matrices (can be changed using ``hicMergeMatrixBins``) and the considered range. The smaller the bin size of the matrices, the finer the differences you score. The *Range* parameter should be selected at a meaningful genomic scale according to, for example, the mean size of the TADs in the organism you work with or to specific ranges found using ``hicPlotDistVsCounts``.
103
104 _________________
105
106 Usage
100 ----- 107 -----
101 108
102 Parameters 109 It is recommended to use this tool on corrected matrices (``hicCorrectMatrix``) at restriction enzyme resolution (unmerged bins).
103 __________ 110
104 - Two contact matrices which are used for the correlation. 111 _________________
105 - Choice if pearson or spearman correlation should be used.
106 - log scale for the values
107 - Correlate full matrix or only specific chromosomes
108 - Correlate only within a given range.
109 - colormap to use: Colormap_
110 112
111 Output 113 Output
112 ------ 114 ------
113 115
114 Pearson correlation 116 **hicCorrelate** outputs correlation plots of multiple Hi-C matrices.
115 ___________________
116 117
117 .. image:: $PATH_TO_IMAGES/hicCorrelate_pearson.png 118 Below, you can find a correlation example of uncorrected Hi-C matrices obtained from *Drosophila melanogaster* embryos, either wild-type or having one gene knocked-down by RNAi.
119
120 Heatmap
121 _______
122
123 .. image:: $PATH_TO_IMAGES/hicCorrelate_Dmel_heatmap.png
118 :width: 45% 124 :width: 45%
119 125
120 .. image:: $PATH_TO_IMAGES/hicCorrelate_pearson_scatter.png 126 This example is showing a heatmap that was calculated using the Pearson correlation of corrected Hi-C matrices with a bin size of 6000 bp at a range of 5000 to 200000. The dendrogram indicates which samples are most similar to each other. You can see that the wild-type samples are seperated from the knock-down samples. In that case, Spearman correlation gives very similar results (not shown).
121 :width: 45%
122 127
128 Scatterplot
129 ___________
123 130
131 .. image:: $PATH_TO_IMAGES/hicCorrelate_Dmel_scatterplot.png
132 :width: 45%
124 133
125 Spearman correlation 134 Additionally, pairwise scatterplots comparing interactions between each sample can be plotted.
126 _____________________
127 135
128 .. image:: $PATH_TO_IMAGES/hicCorrelate_spearman.png 136 _________________
129 :width: 45 %
130
131 .. image:: $PATH_TO_IMAGES/hicCorrelate_spearman_scatter.png
132 :width: 45 %
133 137
134 For more information about HiCExplorer please consider our documentation on readthedocs.io_. 138 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
135 139
136 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 140 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
137 .. _Colormap: https://matplotlib.org/examples/color/colormaps_reference.html 141 .. _Colormap: https://matplotlib.org/examples/color/colormaps_reference.html