Mercurial > repos > xuebing > sharplabtool
comparison tools/rgenetics/rgManQQ.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="rgManQQ1" name="Manhattan/QQ:" version="1.0.3"> | |
| 2 <code file="rgManQQ_code.py"/> | |
| 3 | |
| 4 <description>Plots for WGA P values</description> | |
| 5 | |
| 6 <command interpreter="python"> | |
| 7 rgManQQ.py '$i' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' '$pval_col' '$grey' | |
| 8 </command> | |
| 9 | |
| 10 <inputs> | |
| 11 <page> | |
| 12 <param name="i" type="data" label="Tabular data from your current history" | |
| 13 format="tabular" refresh_on_change="true"/> | |
| 14 </page> | |
| 15 <page> | |
| 16 <param name='name' type='text' size="132" value='Manhattan and QQ plots' label="Title for this job"/> | |
| 17 <param name="pval_col" type='select' size="5" label = 'P value (0-1) column in input file' | |
| 18 dynamic_options="get_phecols(i,False,'pval')" refresh_on_change="true" multiple="true" | |
| 19 help="(Select multiple P value columns for multiple plots holding down the [Ctrl] key as you click)" /> | |
| 20 <param name="chrom_col" type='select' label = 'Chromosome column in input file' | |
| 21 help='Select "None" if chromosome not available or no Manhattan plot required' | |
| 22 dynamic_options="get_phecols(i,True,'chr')" /> | |
| 23 <param name="offset_col" type='select' label = 'Base pair offset column in input file' | |
| 24 help='Select "None" if offset not available or no Manhattan plot required' | |
| 25 dynamic_options="get_phecols(i,True,'offs')" /> | |
| 26 <param name="grey" type="boolean" checked="false" truevalue="true" falsevalue="false" | |
| 27 label="Grey scale for Manhattan plot (default is colour"/> | |
| 28 </page> | |
| 29 </inputs> | |
| 30 | |
| 31 <outputs> | |
| 32 <data format="html" name="out_html" /> | |
| 33 </outputs> | |
| 34 <options refresh="True"/> | |
| 35 | |
| 36 <tests> | |
| 37 <test> | |
| 38 <param name='i' value='smallwgaP.xls' ftype='tabular' > | |
| 39 </param> | |
| 40 <param name='name' value='rgManQQtest1' /> | |
| 41 <param name='pval_col' value='7' /> | |
| 42 <param name='chrom_col' value='1' /> | |
| 43 <param name='offset_col' value='2' /> | |
| 44 <param name='grey' value='0' /> | |
| 45 <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='60'> | |
| 46 <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" | |
| 47 delta = "20000"/> | |
| 48 <extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" | |
| 49 delta = "20000" /> | |
| 50 <extra_files type="file" name='rgManQQtest1.R' value='rgtestouts/rgManQQ/rgManQQtest1.R' compare="diff" lines_diff="160"/> | |
| 51 </output> | |
| 52 </test> | |
| 53 </tests> | |
| 54 <help> | |
| 55 | |
| 56 .. class:: infomark | |
| 57 | |
| 58 **Syntax** | |
| 59 | |
| 60 - **Tabular Data** is a tab delimited header file with chromosome, offset and p values to be plotted | |
| 61 - **Chromosome Column** is the column in that data containing the chromosome as an integer | |
| 62 - **Offset Column** contains the offset within the chromosome | |
| 63 - **P Value Column** contains the (untransformed) p values at that locus - choose multiple columns if needed | |
| 64 | |
| 65 NOTE - plotting millions of p values may take tens of minutes depending on | |
| 66 how busy the server is - be patient please. | |
| 67 | |
| 68 ----- | |
| 69 | |
| 70 .. class:: infomark | |
| 71 | |
| 72 **Summary** | |
| 73 | |
| 74 This tool will create a qq plot and a Manhattan plot for one or more GWA P value columns from a tabular | |
| 75 dataset. For Manhattan plots, the data must include the chromosome (eg use 23,24,25 for x,y,mt...) and | |
| 76 offset. Many analysis files contain the required fields but even without chromosome and offset, a qq plot | |
| 77 can be created. | |
| 78 | |
| 79 ----- | |
| 80 | |
| 81 .. class:: infomark | |
| 82 | |
| 83 **Explanation** | |
| 84 | |
| 85 A "Manhattan" plot shows -log10 p values ordered by offset and by chromosome. Regions with interestingly | |
| 86 improbable p values are above the red line which is drawn at the Bonferroni FWER control level (0.05/n | |
| 87 where n is the number of tests - this is highly conservative for correlated SNPs typical of GWA) | |
| 88 | |
| 89 .. image:: ./static/images/Armitagep_manhattan.png | |
| 90 | |
| 91 A quantile-quantile (QQ) plot is a good way to see systematic departures from the null expectation of | |
| 92 uniform p-values from a genomic analysis. If the QQ plot shows departure from the null (ie a uniform 0-1 | |
| 93 distribution), you hope that this will be in the very smallest p-values suggesting that there might be some | |
| 94 interesting results to look at. A log scale will help emphasise departures from the null at low p values | |
| 95 more clear | |
| 96 | |
| 97 .. image:: ./static/images/Armitagep_qqplot.png | |
| 98 | |
| 99 ----- | |
| 100 | |
| 101 .. class:: infomark | |
| 102 | |
| 103 **Attribution** | |
| 104 | |
| 105 This is a Galaxy tool written by Ross Lazarus. It relies on | |
| 106 ggplot2, an R package from hadley wickham and some | |
| 107 R code for manhattan and qq plots using ggplot2, | |
| 108 borrowed from Stephen Turner found at http://GettingGeneticsDone.blogspot.com/ | |
| 109 | |
| 110 copyright Ross Lazarus 2010 | |
| 111 Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html | |
| 112 but is about as useful as a chocolate teapot without R and Galaxy which all have a | |
| 113 twisty maze of little licenses, all different. | |
| 114 | |
| 115 I'm no lawyer, but it looks like at least LGPL if you create derived works from this code. | |
| 116 Good luck. | |
| 117 | |
| 118 </help> | |
| 119 </tool> |