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120 lines
4.8 KiB
XML
120 lines
4.8 KiB
XML
<tool id="rgManQQ1" name="Manhattan/QQ:" version="1.0.3">
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<code file="rgManQQ_code.py"/>
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<description>Plots for WGA P values</description>
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<command interpreter="python">
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rgManQQ.py '$i' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' '$pval_col' '$grey'
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</command>
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<inputs>
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<page>
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<param name="i" type="data" label="Tabular data from your current history"
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format="tabular" refresh_on_change="true"/>
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</page>
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<page>
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<param name='name' type='text' size="132" value='Manhattan and QQ plots' label="Title for this job"/>
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<param name="pval_col" type='select' size="5" label = 'P value (0-1) column in input file'
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dynamic_options="get_phecols(i,False,'pval')" refresh_on_change="true" multiple="true"
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help="(Select multiple P value columns for multiple plots holding down the [Ctrl] key as you click)" />
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<param name="chrom_col" type='select' label = 'Chromosome column in input file'
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help='Select "None" if chromosome not available or no Manhattan plot required'
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dynamic_options="get_phecols(i,True,'chr')" />
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<param name="offset_col" type='select' label = 'Base pair offset column in input file'
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help='Select "None" if offset not available or no Manhattan plot required'
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dynamic_options="get_phecols(i,True,'offs')" />
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<param name="grey" type="boolean" checked="false" truevalue="true" falsevalue="false"
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label="Grey scale for Manhattan plot (default is colour"/>
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</page>
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</inputs>
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<outputs>
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<data format="html" name="out_html" />
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</outputs>
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<options refresh="True"/>
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<tests>
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<test>
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<param name='i' value='smallwgaP.xls' ftype='tabular' >
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</param>
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<param name='name' value='rgManQQtest1' />
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<param name='pval_col' value='7' />
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<param name='chrom_col' value='1' />
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<param name='offset_col' value='2' />
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<param name='grey' value='0' />
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<output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='60'>
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<extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size"
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delta = "20000"/>
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<extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size"
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delta = "20000" />
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<extra_files type="file" name='rgManQQtest1.R' value='rgtestouts/rgManQQ/rgManQQtest1.R' compare="diff" lines_diff="160"/>
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</output>
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</test>
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</tests>
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<help>
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.. class:: infomark
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**Syntax**
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- **Tabular Data** is a tab delimited header file with chromosome, offset and p values to be plotted
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- **Chromosome Column** is the column in that data containing the chromosome as an integer
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- **Offset Column** contains the offset within the chromosome
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- **P Value Column** contains the (untransformed) p values at that locus - choose multiple columns if needed
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NOTE - plotting millions of p values may take tens of minutes depending on
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how busy the server is - be patient please.
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-----
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.. class:: infomark
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**Summary**
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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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dataset. For Manhattan plots, the data must include the chromosome (eg use 23,24,25 for x,y,mt...) and
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offset. Many analysis files contain the required fields but even without chromosome and offset, a qq plot
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can be created.
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-----
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.. class:: infomark
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**Explanation**
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A "Manhattan" plot shows -log10 p values ordered by offset and by chromosome. Regions with interestingly
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improbable p values are above the red line which is drawn at the Bonferroni FWER control level (0.05/n
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where n is the number of tests - this is highly conservative for correlated SNPs typical of GWA)
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.. image:: ./static/images/Armitagep_manhattan.png
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A quantile-quantile (QQ) plot is a good way to see systematic departures from the null expectation of
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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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distribution), you hope that this will be in the very smallest p-values suggesting that there might be some
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interesting results to look at. A log scale will help emphasise departures from the null at low p values
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more clear
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.. image:: ./static/images/Armitagep_qqplot.png
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-----
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.. class:: infomark
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**Attribution**
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This is a Galaxy tool written by Ross Lazarus. It relies on
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ggplot2, an R package from hadley wickham and some
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R code for manhattan and qq plots using ggplot2,
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borrowed from Stephen Turner found at http://GettingGeneticsDone.blogspot.com/
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copyright Ross Lazarus 2010
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Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html
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but is about as useful as a chocolate teapot without R and Galaxy which all have a
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twisty maze of little licenses, all different.
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I'm no lawyer, but it looks like at least LGPL if you create derived works from this code.
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Good luck.
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</help>
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</tool>
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