Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

annotate hicPlotMatrix.xml @ 10:ca631354e522 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 03:09:39 -0400
parents 79d10df2108e
children 4053214bebac
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1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>plot a Hi-C contact matrix heatmap</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotMatrix</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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10 #if str($pca_conditional.pca_type) == 'bigwig':
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11 ln -s $pca_conditional.pca_bigwig pca.bw &&
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12 #set $pca = '--bigwig pca.bw'
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13 #elif str($pca_conditional.pca_type) == '':
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14 #set $pca = ''
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15 #end if
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16
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17 @BINARY@
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19 --matrix '$matrix_h5_cooler'
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21 #if $title and $title is not None:
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22 --title '$title'
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23 #end if
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25 #if $scoreName and $scoreName is not None:
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26 --scoreName '$scoreName'
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27 #end if
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29 --outFileName plot.$image_file_format
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31 $perChromosome
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32 $clearMaskedBins
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34 ## special: --chromosomeOrder is optional, but if given needs at least one argument
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35 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
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36 #if chroms:
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37 --chromosomeOrder "$chroms"
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38 #end if
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39
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40 #if $region:
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41 --region '$region'
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42 #end if
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44 #if $region2:
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45 --region2 '$region2'
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46 #end if
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47 $log1p
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48 $log
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50 #if $colormap:
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51 --colorMap $colormap
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52 #end if
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54 #if $vMin:
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55 --vMin $vMin
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56 #end if
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58 #if $vMax:
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59 --vMax $vMax
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60 #end if
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62 $pca
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63
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64 && mv plot.$image_file_format plot
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65 ]]>
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66 </command>
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67 <inputs>
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68 <expand macro='matrix_h5_cooler_macro' />
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69
0
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70 <param argument="--title" type="text" optional="true" label="Plot title"/>
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71 <param argument="--scoreName" type="text" optional="true" label="Score name" help="The label for the heatmap legend."/>
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72 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
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73 label="Plot per chromosome"
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74 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
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75 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
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76 label="Remove masked bins from the matrix" />
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77
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78 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):"
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79 help="This option overrides --region and --region2" >
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80 <param name="chromosome" type="text" >
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81 <validator type="empty_field" />
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82 </param>
0
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83 </repeat>
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84
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85 <param argument="--region" type="text" optional="True" label="Plot only this region"
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86 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/>
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87 <param argument="--region2" type="text" optional="True" label="Region two to plot"
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88 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
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89 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended."/>
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90 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/>
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91
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92 <expand macro="colormap" />
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93
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94 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/>
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95 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/>
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96
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97 <conditional name="pca_conditional">
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98 <param name='pca_type' label='Datatype of eigenvector file' type='select'>
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99 <option value='' selected="true"></option>
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100 <option value='bigwig'>bigwig</option>
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101 </param>
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102 <when value='' />
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103 <when value='bigwig'>
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104 <param name='pca_bigwig' type="data" format="bigwig"
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105 label="Eigenvector file"/>
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106 </when>
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107 </conditional>
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108 <param name="image_file_format" type="select" label="Image output format">
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109 <option value="png" selected="True">png</option>
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110 <option value="svg">svg</option>
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111 </param>
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112 </inputs>
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113 <outputs>
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114 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
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115 <change_format>
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116 <when input="image_file_format" value="svg" format="svg" />
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117 </change_format>
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118 </data>
0
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119 </outputs>
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120 <tests>
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121 <test>
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122 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
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123 <conditional name="pca_conditional">
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124 <param name="pca_type" value=''/>
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125 </conditional>
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126 <param name="region" value="chrX:3000000-3500000"/>
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127 <param name="region2" value="chrX:3100000-3600000"/>
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128 <param name="log1p" value="True"/>
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129 <param name="clearMaskedBins" value="True"/>
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130 <param name="image_file_format" value="png" />
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131 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
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132 </test>
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133 <test>
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134 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool"/>
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135 <conditional name="pca_conditional">
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136 <param name="pca_type" value=''/>
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137 </conditional>
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138 <param name="region" value="X:3000000-3500000"/>
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139 <param name="image_file_format" value="png" />
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140 <output name="outFileName" file="Li_chrX30-35_cool.png" ftype="png" compare="sim_size"/>
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141 </test>
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142 <test>
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143 <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/>
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144 <param name="perChromosome" value="True"/>
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145 <conditional name="pca_conditional">
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146 <param name="pca_type" value='bigwig'/>
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147 <param name="pca_bigwig" value="pca1.bw"/>
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148 </conditional>
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149 <param name='colormap' value='hot'/>
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150 <param name="image_file_format" value="svg" />
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151 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
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152 </test>
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153 <test>
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154 <param name="matrix_h5_cooler" value="pearson_small_50kb.h5"/>
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155 <param name="perChromosome" value="True"/>
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156 <conditional name="pca_conditional">
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157 <param name="pca_type" value='bigwig'/>
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158 <param name="pca_bigwig" value="pca1.bw"/>
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159 </conditional>
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160 <param name='colormap' value='hot'/>
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161
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162 <param name="image_file_format" value="svg" />
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163 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
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164 </test>
0
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165 </tests>
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166 <help><![CDATA[
5
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167 Contact matrix plot
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168 =======================
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170 **hicPlotMatrix** is a visualization tool for Hi-C contact matrices. It supports to plot genome-wide contact matrices, one or multiple chromosomes, a region or two regions against each other.
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171 Additionally it can plot the result of a principal component analysis obtained by ``hicPCA`` to have a better understanding of A / B compartments.
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173 _________________
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175 Usage
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176 -----
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178 This tool can be used on any h5 or cool Hi-C contact matrix. It is noteworthy that for comparisons of 2 matrices or more, they must all have the same or similar number of contacts.
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180 _________________
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182 Output
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183 ------
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185 **hicPlotMatrix** outputs a heatmap of a contact matrix in either png or svg format, below is an example of such a plot:
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187 .. image:: $PATH_TO_IMAGES/hicPlotMatrix.png
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188 :width: 50%
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190 Contact matrix of *Drosophila melanogaster* embryos visualized using **hicPlotMatrix**. Hi-C matrix bins were merged to a 25 kb bin size using ``hicMergeMatrixBins`` and the matrix has then been corrected using ``hicCorrectMatrix`` before plotting.
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192 Another example is available below using Hi-C data published by `Lieberman-Aiden <https://doi.org/10.1126/science.1181369>`_ in 2009, (`GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_). A Hi-C contact matrix has been plotted with the ``--perChr`` option and the first eigenvector (pca1) computed by ``hicPCA``. For this plot a pearson correlated matrix was used, which is computed by first creating an observed / expected matrix and then a pearson correlation matrix with ``hicTransform``.
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194 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png
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195 :width: 70 %
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197 _________________
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199 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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201 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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202 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
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203 ]]></help>
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204 <expand macro="citations" />
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205 </tool>