[2] | 1 | <tool id="rgManQQ1" name="Manhattan/QQ:" version="1.0.1"> |
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| 2 | <code file="rgManQQ_code.py"/> |
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| 3 | |
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| 4 | <description>Plots for WGA P values</description> |
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| 5 | |
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| 6 | <command interpreter="python"> |
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| 7 | rgManQQ.py '$i' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' '$pval_col' '$grey' |
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| 8 | </command> |
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| 9 | |
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| 10 | <inputs> |
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| 11 | <page> |
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| 12 | <param name="i" type="data" label="Tabular data from your current history" |
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| 13 | format="tabular" refresh_on_change="true"/> |
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| 14 | </page> |
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| 15 | <page> |
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| 16 | <param name='name' type='text' size="132" value='Manhattan and QQ plots' label="Title for this job"/> |
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| 17 | <param name="pval_col" type='select' size="5" label = 'P value (0-1) column in input file' |
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| 18 | dynamic_options="get_phecols(i,False,'pval')" refresh_on_change="true" multiple="true" |
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| 19 | help="(Select multiple P value columns for multiple plots holding down the [Ctrl] key as you click)" /> |
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| 20 | <param name="chrom_col" type='select' label = 'Chromosome column in input file' |
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| 21 | help='Select "None" if chromosome not available or no Manhattan plot required' |
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| 22 | dynamic_options="get_phecols(i,True,'chr')" /> |
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| 23 | <param name="offset_col" type='select' label = 'Base pair offset column in input file' |
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| 24 | help='Select "None" if offset not available or no Manhattan plot required' |
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| 25 | dynamic_options="get_phecols(i,True,'offs')" /> |
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| 26 | <param name="grey" type="boolean" checked="false" truevalue="true" falsevalue="false" |
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| 27 | label="Grey scale for Manhattan plot (default is colour"/> |
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| 28 | </page> |
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| 29 | </inputs> |
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| 30 | |
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| 31 | <outputs> |
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| 32 | <data format="html" name="out_html" /> |
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| 33 | </outputs> |
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| 34 | <options refresh="True"/> |
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| 35 | |
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| 36 | <tests> |
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| 37 | <test> |
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| 38 | <param name='i' value='smallwgaP.xls' ftype='tabular' > |
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| 39 | </param> |
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| 40 | <param name='name' value='rgManQQtest1' /> |
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| 41 | <param name='pval_col' value='7' /> |
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| 42 | <param name='chrom_col' value='1' /> |
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| 43 | <param name='offset_col' value='2' /> |
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| 44 | <param name='grey' value='0' /> |
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| 45 | <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='40'> |
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| 46 | <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" |
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| 47 | delta = "10000"/> |
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| 48 | <extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" |
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| 49 | delta = "10000" /> |
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| 50 | <extra_files type="file" name='rgManQQtest1.R' value='rgtestouts/rgManQQ/rgManQQtest1.R' compare="diff" lines_diff="160"/> |
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| 51 | </output> |
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| 52 | </test> |
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| 53 | </tests> |
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| 54 | <help> |
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| 55 | |
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| 56 | .. class:: infomark |
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| 57 | |
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| 58 | **Syntax** |
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| 59 | |
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| 60 | - **Tabular Data** is a tab delimited header file with chromosome, offset and p values to be plotted |
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| 61 | - **Chromosome Column** is the column in that data containing the chromosome as an integer |
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| 62 | - **Offset Column** contains the offset within the chromosome |
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| 63 | - **P Value Column** contains the (untransformed) p values at that locus - choose multiple columns if needed |
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| 64 | |
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| 65 | NOTE - plotting millions of p values may take tens of minutes depending on |
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| 66 | how busy the server is - be patient please. |
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| 67 | |
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| 68 | ----- |
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| 69 | |
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| 70 | .. class:: infomark |
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| 71 | |
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| 72 | **Summary** |
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| 73 | |
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| 74 | This tool will create a qq plot and a Manhattan plot for one or more GWA P value columns from a tabular |
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| 75 | dataset. For Manhattan plots, the data must include the chromosome (eg use 23,24,25 for x,y,mt...) and |
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| 76 | offset. Many analysis files contain the required fields but even without chromosome and offset, a qq plot |
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| 77 | can be created. |
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| 78 | |
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| 79 | ----- |
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| 80 | |
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| 81 | .. class:: infomark |
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| 82 | |
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| 83 | **Explanation** |
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| 84 | |
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| 85 | A "Manhattan" plot shows -log10 p values ordered by offset and by chromosome. Regions with interestingly |
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| 86 | improbable p values are above the red line which is drawn at the Bonferroni FWER control level (0.05/n |
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| 87 | where n is the number of tests - this is highly conservative for correlated SNPs typical of GWA) |
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| 88 | |
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| 89 | .. image:: ../static/images/Armitagep_manhattan.png |
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| 90 | |
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| 91 | A quantile-quantile (QQ) plot is a good way to see systematic departures from the null expectation of |
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| 92 | uniform p-values from a genomic analysis. If the QQ plot shows departure from the null (ie a uniform 0-1 |
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| 93 | distribution), you hope that this will be in the very smallest p-values suggesting that there might be some |
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| 94 | interesting results to look at. A log scale will help emphasise departures from the null at low p values |
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| 95 | more clear |
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| 96 | |
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| 97 | .. image:: ../static/images/Armitagep_qqplot.png |
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| 98 | |
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| 99 | ----- |
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| 100 | |
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| 101 | .. class:: infomark |
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| 102 | |
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| 103 | **Attribution** |
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| 104 | |
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| 105 | This is a Galaxy tool written by Ross Lazarus. It relies on |
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| 106 | ggplot2, an R package from hadley wickham and some |
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| 107 | R code for manhattan and qq plots using ggplot2, |
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| 108 | borrowed from Stephen Turner found at http://GettingGeneticsDone.blogspot.com/ |
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| 109 | |
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| 110 | copyright Ross Lazarus 2010 |
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| 111 | Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html |
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| 112 | but is about as useful as a chocolate teapot without R and Galaxy which all have a |
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| 113 | twisty maze of little licenses, all different. |
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| 114 | |
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| 115 | I'm no lawyer, but it looks like at least LGPL if you create derived works from this code. |
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| 116 | Good luck. |
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| 117 | |
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| 118 | </help> |
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| 119 | </tool> |
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