annotate hicPCA.xml @ 14:3b5b54ed6392 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:05:22 +0000
parents c435572f7cf1
children 41dbf4d162a2
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1 <tool id="hicexplorer_hicpca" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>compute the principal components for A / B compartment analysis</description>
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3 <macros>
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4 <token name="@BINARY@">hicPCA</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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9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
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10 @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext'
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12 @CHROMOSOME_LIST@
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14 --outputFileName pca1.$outputFormat pca2.$outputFormat
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15 --format $outputFormat
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17 #if $ligation_factor:
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18 $ligation_factor
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19 #end if
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21 #if $ignoreMaskedBins:
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22 $ignoreMaskedBins
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23 #end if
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25 #if $extra_track_conditional.extra_track_selection == 'gene_density':
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26 --extraTrack '$extra_track_conditional.extraTrack'
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27 #elif $extra_track_conditional.extra_track_selection == 'histon_mark':
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28 --extraTrack '$extra_track_conditional.extraTrack'
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29 --histonMarkType '$extra_track_conditional.histonMarkType'
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30 #end if
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32 #if $pearsonMatrix:
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33 --pearsonMatrix pearson.$matrix_h5_cooler.ext
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34 #end if
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36 #if $obsexpMatrix:
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37 --obsexpMatrix obsexp.$matrix_h5_cooler.ext
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38 #end if
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40 && mv pca1.$outputFormat pca1
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41 && mv pca2.$outputFormat pca2
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42 #if $pearsonMatrix:
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43 && mv pearson.$matrix_h5_cooler.ext pearson
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44 #end if
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46 #if $obsexpMatrix:
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47 && mv obsexp.$matrix_h5_cooler.ext obsexp
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48 #end if
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49
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50 ]]>
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51 </command>
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52 <inputs>
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53 <expand macro='matrix_h5_cooler_macro' />
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54 <param name='outputFormat' type='select' label="Output file format">
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55 <option value='bigwig' selected="true">bigwig</option>
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56 <option value="bedgraph">bedgraph</option>
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57 </param>
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58
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59 <expand macro="chromosome_list" />
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61 <param name='ligation_factor' type='boolean' truevalue='--ligation_factor' label='Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation' />
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62 <param name='ignoreMaskedBins' type='boolean' truevalue='--ignoreMaskedBins' label='This option removes the masked bins before the PCA is computed' />
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63
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64 <conditional name="extra_track_conditional">
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65 <param name='extra_track_selection' label='Extra track type' type='select'>
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66 <option value='' selected='true'>No track</option>
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67 <option value='gene_density'>Gene density</option>
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68 <option value='histon_mark'>Histon mark coverage</option>
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69 </param>
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70 <when value='gene_density' >
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71 <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histon marks to flip sign' />
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72 </when>
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73 <when value='histon_mark'>
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74 <param name='extraTrack' type='data' format='bed,bigwig' label='Correlate PCA with e.g. gene density or histon marks to flip sign' />
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75 <param name='histonMarkType' type='select' label="Histon mark type">
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76 <option value='active' selected="true">active</option>
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77 <option value="inactive">inactive</option>
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78 </param>
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79 </when>
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80 <when value='' />
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81 </conditional>
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82 <param argument='--pearsonMatrix' type='boolean' truevalue='--pearsonMatrix' falsevalue='' label='Return internally used Pearson matrix' />
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83 <param argument='--obsexpMatrix' type='boolean' truevalue='--obsexpMatrix' falsevalue='' label='Return internally used observed / expected matrix' />
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84
0
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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85 </inputs>
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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86 <outputs>
4
38a612a120a8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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87 <data name="pca1" from_work_dir="pca1" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC1">
2
97c797606746 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
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88 <change_format>
97c797606746 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
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89 <when input="outputFormat" value="bedgraph" format="bedgraph" />
97c797606746 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
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90 </change_format>
0
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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91 </data>
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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92 <data name="pca2" from_work_dir="pca2" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC2">
2
97c797606746 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
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93 <change_format>
97c797606746 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
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94 <when input="outputFormat" value="bedgraph" format="bedgraph" />
97c797606746 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
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95 </change_format>
0
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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96 </data>
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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97
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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98 <data name="pearson_outfile" from_work_dir="pearson" format="cool">
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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99 <filter>pearsonMatrix</filter>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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100 <change_format>
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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101 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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102 </change_format>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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103 </data>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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104 <data name="obsexp_outfile" from_work_dir="obsexp" format="cool">
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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105 <filter>obsexpMatrix</filter>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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106 <change_format>
14
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107 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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108 </change_format>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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109 </data>
0
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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110 </outputs>
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111 <tests>
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112 <test>
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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113 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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114 <param name="outputFormat" value="bigwig" />
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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115 <conditional name="extra_track_conditional">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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116 <param name="extra_track_selection" value="" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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117 </conditional>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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118
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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119 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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120 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
121 </test>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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122 <test>
14
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123 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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124 <param name="outputFormat" value="bigwig" />
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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125 <param name="ligation_factor" value="True" />
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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126
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
127 <conditional name="extra_track_conditional">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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diff changeset
128 <param name="extra_track_selection" value="" />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
129 </conditional>
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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130
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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diff changeset
131 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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132 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
133 </test>
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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134 <test>
14
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135 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
136 <param name="outputFormat" value="bigwig" />
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
137 <param name="ignoreMaskedBins" value="True" />
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
138
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
139 <conditional name="extra_track_conditional">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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140 <param name="extra_track_selection" value="" />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
141 </conditional>
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
142
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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143 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' />
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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144 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
145 </test>
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
146 <test>
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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147 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
148 <param name="outputFormat" value="bigwig" />
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
149 <conditional name="extra_track_conditional">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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150 <param name="extra_track_selection" value="gene_density" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
151 <param name="extraTrack" value="dm3_genes.bed.gz" />
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
152 </conditional>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
153
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
154 <repeat name="chromosome_list">
14
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155 <param name="chromosomes" value="chrX" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
156 </repeat>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
157 <repeat name="chromosome_list">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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158 <param name="chromosomes" value="chrXHet" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
159 </repeat>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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160
14
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161 <output name="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta='40000' />
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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162 <output name="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta='40000' />
0
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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163 </test>
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164 <test>
14
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165 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
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167 <param name="outputFormat" value="bigwig" />
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168 <conditional name="extra_track_conditional">
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169 <param name="extra_track_selection" value="" />
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170 </conditional>
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171 <param name='pearsonMatrix' value='True' />
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172 <param name='obsexpMatrix' value='True' />
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174 <repeat name="chromosome_list">
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175 <param name="chromosomes" value="chrX" />
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176 </repeat>
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177 <repeat name="chromosome_list">
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178 <param name="chromosomes" value="chrXHet" />
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179 </repeat>
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180
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181 <output name="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta='40000' />
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182 <output name="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta='40000' />
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183
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184 <output name="pearson_outfile" ftype="h5">
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185 <assert_contents>
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186 <has_h5_keys keys='intervals,matrix' />
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187 </assert_contents>
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188 </output>
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189 <output name="obsexp_outfile" ftype="h5">
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190 <assert_contents>
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191 <has_h5_keys keys='intervals,matrix' />
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192 </assert_contents>
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193 </output>
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194 </test>
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195 </tests>
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196 <help><![CDATA[
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197
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198 Principal component analysis
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199 ============================
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200
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201 `Lieberman-Aiden et al. (2009)`_ demonstrated that open and closed chromatin domains throughout the genome occupy different spatial compartments in the nucleus, defined as A (activate) and B (inactive) compartments.
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202
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203 **hicPCA** computes two eigenvector files based on the input matrix for an A / B compartment analysis following the computation steps detailed by `Lieberman-Aiden et al. (2009)`_: the transformation of the contact matrix
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204 into an observed vs. expected matrix and consecutively a Pearson correlation matrix shows a plaid pattern. These plaid pattern are called A and B. Applying a PCA on the Pearson correlation matrix gives the eigenvectors
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205 and Lieberman-Aiden shows that the values of the eigenvectors correspond to the distribution of genes and with features of open and closed chromatin. In some cases the first principal component corresponds to the two
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206 chromosomes arms and the second eigenvector to the plaid pattern. Therefore always the first two principal components needs to be returned and investigated.
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207
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208 _________________
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209
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210 Usage
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211 -----
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212
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213 This tool must be used on Hi-C contact matrices with large bins (over 20kb) using ``hicMergeMatrixBins`` and corrected with ``hicCorrectMatrix``. Using matrices with a too high resolution (small bins or at restriction enzyme resolution) might take several days to run (even with over 100 CPU) or will fail due to memory limitations.
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214
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215 _________________
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217 Output
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218 ------
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219 Two files are outputed by **hicPCA**, one with the first (pca1) and one with the second (pca2) eigenvector as bigwig or bedgraph. These files can be plotted alongside Hi-C heatmaps, gene density or external datasets such as open chromatin or histone marks enrichment using ``pyGenomeTracks`` or ``hicPlotMatrix``.
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220
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221 For example, below you can find a ``hicPlotMatrix`` of the Pearson correlation matrix derived from a contact matrix for chromosome 6 in mouse computed with ``hicTransform`` (which is part of A/B compartments computation). The optional data track at the bottom shows the first eigenvector for A/B compartment obtained using **hicPCA**.
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222
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223 .. image:: $PATH_TO_IMAGES/hicPCA.png
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224 :scale: 35 %
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226 _________________
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228 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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230 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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231 .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
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232 ]]> </help>
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233 <expand macro="citations" />
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234 </tool>