| Previous changeset 6:8926550196ce (2018-03-07) Next changeset 8:18737f03d581 (2018-04-27) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 |
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modified:
hicMergeMatrixBins.xml macros.xml test-data/compare_matrices_log2ratio.h5 test-data/compare_matrices_pearson_ratio.cool test-data/covariance_small_50kb.cool test-data/covariance_small_50kb.h5 test-data/hicCorrectMatrix_result1.npz.h5 test-data/hicMergeMatrixBins_result1.npz.h5 test-data/hicPlotDistVsCounts_result2.png test-data/hicSumMatrices_result1.npz.h5 test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/obs_exp_small_50kb.cool test-data/obs_exp_small_50kb.h5 test-data/pca1.bw test-data/pearson_small_50kb.h5 test-data/pearson_small_50kb_transform.cool test-data/small_matrix_50kb_pearson_pca1_plot.svg test-data/small_test_matrix_2.h5 |
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added:
static/images/hicAggregateContacts.png static/images/hicCompareMatrices_QC_log2_m50_matrix_plot (1).png static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot (1).png static/images/hicCorrelate_Dmel_heatmap.png static/images/hicCorrelate_Dmel_scatterplot.png static/images/hicMergeMatrixBins_Xchr.png static/images/hicMergeMatrixBins_Xregion.png static/images/hicPCA.png static/images/hicPlotDistvsCounts.png static/images/hicPlotMatrix.png static/images/hicPlotTADs.png static/images/hicQC_distance.png static/images/hicQC_pairs_discarded.png static/images/hicQC_pairs_sequenced.png static/images/hicQC_read_orientation.png static/images/hicQC_unmappable_and_non_unique.png static/images/pulication_plots_viewpoint.png |
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removed:
involucro macros.xml.orig test-data/multiFDR_zscore_matrix.h5 |
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| diff -r 8926550196ce -r c14ba4629233 hicMergeMatrixBins.xml --- a/hicMergeMatrixBins.xml Wed Mar 07 03:45:11 2018 -0500 +++ b/hicMergeMatrixBins.xml Fri Apr 27 03:38:09 2018 -0400 |
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| @@ -1,5 +1,5 @@ <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0"> - <description>Merges bins from a Hi-C matrix</description> + <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</description> <macros> <token name="@BINARY@">hicMergeMatrixBins</token> <import>macros.xml</import> @@ -19,7 +19,7 @@ <expand macro='matrix_h5_cooler_macro' /> <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" /> - <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" /> + <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." /> <param name='outputFormat' type='select' label="Output file format"> <option value='h5' selected='true'>HiCExplorer format</option> <option value="cool">cool</option> @@ -44,31 +44,51 @@ Change matrix resolution ======================== -``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb +**hicMergeMatrixBins** is used to decrease the resolution of a matrix. With this tool, you can for example create out of a 100 kb contact matrix a 1000 kb one: Number of bins to merge = 10 100 kb * 10 = 1000 kb = 1 Mb -This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is -to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but -to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it -difficult to interpret, especially if the read depth of the Hi-C data is not high. +Depending on the downstream analyses to perform on a Hi-C matrix generated with HiCExplorer, one might need different bin resolutions. For example using ``hicPlotMatrix`` to display chromatin interactions of a whole chromosome will not produce any meaningful vizualisation if it is performed on a matrix at restriction sites resolution (unmerged). Furthermore, the higher the resolution of a matrix, the more detailed it is, which can make it +difficult to interpret, especially if the read depth of the Hi-C data is not high enough. **hicMergeMatrixBins** address these issues by merging a given number of adjacent bins to reduce Hi-C matrices resolution. -Input +_________________ + +Usage ----- -Parameters -__________ -- contact matrix to change the resolution on -- Number of bins to merge -- running window +To limit the loss of information, it is mandatory to perform **hicMergeMatrixBins** on matrices prior to any correction and any other bin merging (direct output from ``hicBuildMatrix``). After bin merging, ``hicCorrectMatrix`` must be used for downstream analyses requiring corrected matrices. + +_________________ Output ------ -A contact matrix with the resolution ``original resolution * number of bins``. +**hicMergeMatrixBins** outputs a Hi-C matrix with reduced resolution. + +Below, we will develop the example of a Hi-C matrix in *Drosophila melanogaster* that we want to display at the whole X-chromosome scale and at the scale of a 1Mb region of the X chromosome. To do this, we performed two different bin merging using **hicMergeMatrixBins** on an uncorrected matrix built at the restiction sites resolution using ``hicBuildMatrix``. + +Starting from a matrix with bins of a median length of 529bp (restriction enzyme resolution, here DpnII), running **hicMergeMatrixBins** with a number of bins to merge of 3 produced a matrix with bins of a median length of 1661bp, while **hicMergeMatrixBins** with a number of bins to merge of 50 produced a matrix with bins of a median length of 29798bp. + +After the correction of these three matrices using ``hicCorrectMatrix``, we plotted them using ``hicPlotMatrix`` at the scale of the whole X-chromosome and at the scale of the X:2000000-3000000 region to see the effect of bin merging on the interactions visualization. + +- **Effect of bins merging at the scale of a chromosome:** + +.. image:: $PATH_TO_IMAGES/hicMergeMatrixBins_Xchr.png + :width: 60 % + +When observed altogether, the plots above show that the merging of bins by 50 is the most adequate way to plot interactions for a whole chromosome in *Drosophila melanogaster* when starting from a matrix with bins of a median length of 529bp. + +- **Effect of bins merging at the scale of a specific region:** + +.. image:: $PATH_TO_IMAGES/hicMergeMatrixBins_Xregion.png + :width: 60 % + +When observed altogether, the plots above show that the merging of bins by 3 is the most adequate way to plot interactions for a region of 1Mb in Drosophila melanogaster when starting from a matrix with bins of a median length of 529bp. + +_________________ | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
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| diff -r 8926550196ce -r c14ba4629233 involucro |
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| Binary file involucro has changed |
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| diff -r 8926550196ce -r c14ba4629233 macros.xml --- a/macros.xml Wed Mar 07 03:45:11 2018 -0500 +++ b/macros.xml Fri Apr 27 03:38:09 2018 -0400 |
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| @@ -1,7 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">2.1</token> - + <token name="@WRAPPER_VERSION@">2.1.2</token> <token name="@USE_RANGE@"> #if $use_range.select_use_range == "yes_use_range": --range $range_min:$range_max @@ -28,7 +27,7 @@ </xml> <xml name="use_range"> <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> - <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range"> + <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered."> <option value="no_use_range">No restriction</option> <option value="yes_use_range">Only consider counts within a range</option> </param> @@ -40,8 +39,8 @@ </xml> <xml name="range"> - <param name="range_min" type="integer" value="" min="0"/> - <param name="range_max" type="integer" value="" min="0"/> + <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/> + <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/> </xml> <xml name="colormap"> @@ -189,9 +188,9 @@ <xml name="multiple_input_matrices"> - <repeat name="input_files" title="HiC Matrix files" min="2"> + <repeat name="input_files" title="Hi-C Matrix files" min="2"> <param name="matrix" type="data" format="h5,cool" - label="HiC Matrix file" + label="Hi-C Matrix file" help=""/> <param name="mlabel" type="text" size="30" optional="true" value="" label="Label" |
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| diff -r 8926550196ce -r c14ba4629233 macros.xml.orig --- a/macros.xml.orig Wed Mar 07 03:45:11 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,585 +0,0 @@\n-<macros>\n- <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n-<<<<<<< HEAD\n- <token name="@WRAPPER_VERSION@">2.0</token>\n-\n- <token name="@USE_RANGE@">\n- #if $use_range.select_use_range == "yes_use_range":\n- --range $range_min:$range_max\n- #end if\n- </token>\n-\n-=======\n- <token name="@WRAPPER_VERSION@">2.1alpha1</token>\n->>>>>>> joachimwolff-master\n- <xml name="requirements">\n- <requirements>\n- <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n- <yield />\n- </requirements>\n- <version_command>@BINARY@ --version</version_command>\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.5281/zenodo.1133705</citation>\n- <yield />\n- </citations>\n- </xml>\n-\n- <xml name="zMax">\n- <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->\n- </xml>\n- <xml name="use_range">\n- <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->\n- <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">\n- <option value="no_use_range">No restriction</option>\n- <option value="yes_use_range">Only consider counts within a range</option>\n- </param>\n- <when value="no_use_range"/>\n- <when value="yes_use_range">\n- <param name="range_min" type="integer" value="" min="0"/>\n- <param name="range_max" type="integer" value="" min="0"/>\n- </when>\n- </conditional>\n- </xml>\n- <xml name="colormap">\n- <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n- <option value="RdYlBu">RdYlBu</option>\n- <option value="Accent">Accent</option>\n- <option value="Spectral">Spectral</option>\n- <option value="Set1">Set1</option>\n- <option value="Set2">Set2</option>\n- <option value="Set3">Set3</option>\n- <option value="Dark2">Dark2</option>\n- <option value="Reds">Reds</option>\n- <option value="Oranges">Oranges</option>\n- <option value="Greens">Greens</option>\n- <option value="Blues">Blues</option>\n- <option value="Greys">Greys</option>\n- <option value="Purples">Purples</option>\n- <option value="Paired">Paired</option>\n- <option value="Pastel1">Pastel1</option>\n- <option value="Pastel2">Pastel2</option>\n- <option value="spring">spring</option>\n- <option value="summer">summer</option>\n- <option value="autumn">autumn</option>\n- <option value="winter">winter</option>\n- <option value="hot">hot</option>\n- <option value="coolwarm">coolwarm</option>\n- <option value="cool">cool</option>\n- <option value="seismic">seismic</option>\n- <option value="terrain">terrain</option>\n- <option value="ocean">ocean</option>\n- <option value="rainbow">rainbow</option>\n- <option value="bone">bone</option>\n- <option value="flag">flag</option>\n- <option value="prism">prism</option>\n- <option value="cubehelix">cubehelix</option>\n- <option value="binary">binary</option>\n- <option value="pink">pink</option>\n- <option value="gray">gray</option>\n- <option value="copper">copper</option>\n- <option value="BrBG">BrBG</option>\n- <option value="BuGn">BuGn</option>\n- <option value="'..b'/>\n- <when value="yes">\n- <yield />\n- <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>\n- <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n- </when>\n- </conditional>\n- </xml>\n-\n- <xml name="input_image_file_format">\n- <param name="outFileFormat" type="select" label="Image file format">\n- <option value="png" selected="true">png</option>\n- <option value="pdf">pdf</option>\n- <option value="svg">svg</option>\n- <option value="eps">eps</option>\n- <option value="emf">emf</option>\n- </param>\n- </xml>\n-\n- <xml name="output_image_file_format">\n- <data format="png" name="outFileName" label="${tool.name} image">\n- <change_format>\n- <when input="output.outFileFormat" value="pdf" format="pdf" />\n- <when input="output.outFileFormat" value="svg" format="svg" />\n- <when input="output.outFileFormat" value="eps" format="eps" />\n- <when input="output.outFileFormat" value="emf" format="emf" />\n- </change_format>\n- </data>\n- </xml>\n-\n- <xml name="output_save_matrix_values">\n- <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">\n- <filter>\n- ((\n- output[\'showOutputSettings\'] == \'yes\' and\n- output[\'saveMatrix\'] is True\n- ))\n- </filter>\n- </data>\n- </xml>\n-\n- <xml name="output_graphic_outputs">\n- <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">\n- <filter>\n- ((\n- output[\'showOutputSettings\'] == \'yes\' and\n- output[\'saveData\'] is True\n- ))\n- </filter>\n- </data>\n- <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">\n- <filter>\n- ((\n- output[\'showOutputSettings\'] == \'yes\' and\n- output[\'saveSortedRegions\'] is True\n- ))\n- </filter>\n- </data>\n- </xml>\n-\n- <xml name="track_input_h5_macro">\n- <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>\n- </xml>\n- <xml name="track_input_bed_macro">\n- <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>\n- </xml>\n- <xml name="track_input_bedgraph_macro">\n- <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>\n- </xml>\n- <xml name="track_input_bigwig_macro">\n- <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>\n- </xml>\n- <xml name="track_input_bedgraph_matrix_macro">\n- <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>\n- </xml>\n- <xml name="track_input_tabular_macro">\n- <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>\n- </xml>\n- <xml name="plot_title">\n- <param name="title" type="text" optional="true" label="Plot title"/>\n- </xml>\n-\n- <xml name="spacer_macro">\n- <param name="spacer_width" type="float" value="" optional="True"\n- label="Include spacer at the end of the track." help="Width of the spacer." />\n- </xml>\n- <xml name="fontsize_macro">\n- <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />\n- </xml>\n-</macros>\n' |
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| diff -r 8926550196ce -r c14ba4629233 test-data/small_matrix_50kb_pearson_pca1_plot.svg --- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Mar 07 03:45:11 2018 -0500 +++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg Fri Apr 27 03:38:09 2018 -0400 |
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| diff -r 8926550196ce -r c14ba4629233 test-data/small_test_matrix_2.h5 |
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| Binary file test-data/small_test_matrix_2.h5 has changed |
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