root/galaxy-central/tools/rgenetics/rgManQQ.xml

リビジョン 2, 4.8 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="rgManQQ1" name="Manhattan/QQ:" version="1.0.1">
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='40'>
46   <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size"
47     delta = "10000"/>
48   <extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size"
49     delta = "10000" />
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
65NOTE - plotting millions of p values may take tens of minutes depending on
66how busy the server is - be patient please.
67
68-----
69
70.. class:: infomark
71
72**Summary**
73
74This tool will create a qq plot and a Manhattan plot for one or more GWA P value columns from a tabular
75dataset. For Manhattan plots, the data must include the chromosome (eg use 23,24,25 for x,y,mt...) and
76offset. Many analysis files contain the required fields but even without chromosome and offset, a qq plot
77can be created.
78
79-----
80
81.. class:: infomark
82
83**Explanation**
84
85A "Manhattan" plot shows -log10 p values ordered by offset and by chromosome. Regions with interestingly
86improbable p values are above the red line which is drawn at the Bonferroni FWER control level (0.05/n
87where 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
91A quantile-quantile (QQ) plot is a good way to see systematic departures from the null expectation of
92uniform p-values from a genomic analysis. If the QQ plot shows departure from the null (ie a uniform 0-1
93distribution), you hope that this will be in the very smallest p-values suggesting that there might be some
94interesting results to look at. A log scale will help emphasise departures from the null at low p values
95more clear
96
97.. image:: ../static/images/Armitagep_qqplot.png
98
99-----
100
101.. class:: infomark
102
103**Attribution**
104
105This is a Galaxy tool written by Ross Lazarus. It relies on
106ggplot2, an R package from hadley wickham and some
107R code for manhattan and qq plots using ggplot2,
108borrowed from Stephen Turner found at http://GettingGeneticsDone.blogspot.com/
109
110copyright Ross Lazarus 2010
111Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html
112but is about as useful as a chocolate teapot without R and Galaxy which all have a
113twisty maze of little licenses, all different.
114
115I'm no lawyer, but it looks like at least LGPL if you create derived works from this code.
116Good luck.
117
118</help>
119</tool>
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