| Previous changeset 8:d398f5373c70 (2018-03-07) Next changeset 10:9c5ffb1f836f (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:
hicPlotMatrix.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 d398f5373c70 -r 653c6fead9f9 hicPlotMatrix.xml --- a/hicPlotMatrix.xml Wed Mar 07 03:44:12 2018 -0500 +++ b/hicPlotMatrix.xml Fri Apr 27 03:36:47 2018 -0400 |
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| @@ -1,5 +1,5 @@ <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> - <description>Plots a HiC matrix heatmap</description> + <description>plot a Hi-C contact matrix heatmap</description> <macros> <token name="@BINARY@">hicPlotMatrix</token> <import>macros.xml</import> @@ -13,7 +13,7 @@ #elif str($pca_conditional.pca_type) == '': #set $pca = '' #end if - + @BINARY@ --matrix '$matrix_h5_cooler' @@ -68,7 +68,7 @@ <expand macro='matrix_h5_cooler_macro' /> <param argument="--title" type="text" optional="true" label="Plot title"/> - <param argument="--scoreName" type="text" optional="true" label="Score name"/> + <param argument="--scoreName" type="text" optional="true" label="Score name" help="The label for the heatmap legend."/> <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" label="Plot per chromosome" help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" /> @@ -86,13 +86,13 @@ help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/> <param argument="--region2" type="text" optional="True" label="Region two to plot" help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/> - <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/> - <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values."/> + <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."/> + <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/> <expand macro="colormap" /> - <param argument="--vMin" type="float" optional="true" label="vMin"/> - <param argument="--vMax" type="float" optional="true" label="vMax"/> + <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/> + <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/> <conditional name="pca_conditional"> <param name='pca_type' label='Datatype of eigenvector file' type='select'> @@ -101,7 +101,7 @@ </param> <when value='' /> <when value='bigwig'> - <param name='pca_bigwig' type="data" format="bigwig" + <param name='pca_bigwig' type="data" format="bigwig" label="Eigenvector file"/> </when> </conditional> @@ -111,7 +111,7 @@ </param> </inputs> <outputs> - <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${on_string}"> + <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot"> <change_format> <when input="image_file_format" value="svg" format="svg" /> </change_format> @@ -158,7 +158,7 @@ <param name="pca_bigwig" value="pca1.bw"/> </conditional> <param name='colormap' value='hot'/> - + <param name="image_file_format" value="svg" /> <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/> </test> @@ -167,40 +167,35 @@ Contact matrix plot ======================= -``hicPlotMatrix`` is a visualization tool for a contact matrix. It supports to plot the whole contact matrix, one or more chromosomes, a region or two regions against each other. - Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments. +**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. +Additionally it can plot the result of a principal component analysis obtained by ``hicPCA`` to have a better understanding of A / B compartments. -Input +_________________ + +Usage ----- -Parameters -__________ -- the contact matrix: h5 or cool file format. -- A title for the plot -- Score name -- per chromosome -- The chromosomes to include in the plot. -- What to show: -- The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used. -- log / log1p of the values: It is recommended to use log1p. -- Colormaps_ for the heatmap. -- vMin / vMax -- principal component: a bigwig file containing eigenvector information +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. + +_________________ Output ------ -The contact matrix plotted for chromosome 1. +**hicPlotMatrix** outputs a heatmap of a contact matrix in either png or svg format, below is an example of such a plot: -.. image:: SRR027956.svg - :width: 60% +.. image:: $PATH_TO_IMAGES/hicPlotMatrix.png + :width: 50% +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. -The contact matrix used with ``--perChr`` and the first eigenvector from the tool ``hicPCA``. For this plot a pearson correlated matrix was used which is computed by creating first an observed / expected matrix and second a pearson correlation matrix. These matricies can be computed with ``hicChangeMatrixType``. The used Hi-C data were 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>`_. +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``. .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png :width: 70 % +_________________ + | For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html @@ -208,4 +203,3 @@ ]]></help> <expand macro="citations" /> </tool> - |
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| diff -r d398f5373c70 -r 653c6fead9f9 involucro |
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| diff -r d398f5373c70 -r 653c6fead9f9 macros.xml --- a/macros.xml Wed Mar 07 03:44:12 2018 -0500 +++ b/macros.xml Fri Apr 27 03:36:47 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 d398f5373c70 -r 653c6fead9f9 macros.xml.orig --- a/macros.xml.orig Wed Mar 07 03:44:12 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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