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== Get geneZoom Source Codes ==
== Get geneZoom Source Codes ==
=== Download from GitHub with Git ===
=== Download from GitHub with Git ===
After you unzip, you can find 3 directories in "geneZoom" (./example ./lib ./scripts ./ref).
After you unzip, you can find 3 directories in "geneZoom" (./example ./lib ./scripts ./ref).
== Basic Usage Example ==
== Basic Usage Example ==
You can get the help document.
You can get the help document.
== Parameters ==
'''vcf''': The VCF file has SNP information. This VCF must have header with sample ID. It can be a gz file or ASCII file.
'''gene''': The gene region will be plotted. For example, "PCSK9".
'''phenotypeFile''': The phenotype has phenotype value and sample ID. This file must have header to spcify which colum is phenotype value and sample ID.
'''sampleFieldName''': The field name of sample ID in the phenotype file.
'''phenotypeFieldName''': The field name of phenotype value in the phenotype file
'''phenotypeDelim''': The delim in phenotype file. It can be tab, blank or comma.
'''snpList''': SNP list which you want to show in plot. If you have a lot SNPs in the gene region, you can specify the SNPs only shown in the plot. Can be NULL.
'''snpChrFieldName''': The field name of CHR in SNP list. If you don't define snpList, this Can be NULL.
'''snpPosFieldName''': The field name of POS in SNP list. If you don't define snpList, this Can be NULL.
'''snpChrPosFieldName''': The field name of CHR:POS in SNP list. If you don't define snpList, this Can be NULL.
'''snpDelim''': The delim in snp list. It can be tab, blank or comma. If you don't define snpList, this Can be NULL.
'''lableSNPs''': The SNP which will be labled in plot. Can be NULL.
'''flags''': The annotation values, MAF range and colors. For example,splicing:0:0.01:red,readthrough:blue. You must specify annotation value,MAF range and color can be empty. The tool will use the default MAF range(0,0.5), and random select one color.
'''defaultIntron''': The default intron lenght in plot. When draw enxon region, tool re-define the intron region with this value. Can be NULL.
'''title''': The titile of the plot. Can be NULL.
'''xlab''': The xlab of the plot. Can be NULL.
'''ylab''': The xlab of the plot. Can be NULL.
'''titleCex''': The cex of title. This value can change the size of title. Can be NULL.
'''xlabCex''': The cex of xlab. This value can change the size of xlab. Can be NULL.
'''ylabCex''': The cex of ylab. This value can change the size of ylab. Can be NULL.
'''scatterYAxisCex''': The cex of y axis. This value can change the size of y axis. Can be NULL.
'''phenotyeMeanLineColor''': The color of mean value of all SNPs in gene region. Can be NULL.
'''phenotyeMeanLineType''': The line type of mean value of all SNPs in gene region. Can be NULL.
'''phenotyeSDLineColor''': The color of standard deviation value of all SNPs in gene region. Can be NULL.
'''phenotyeSDLineType''': The line type of standard deviation value of all SNPs in gene region. Can be NULL.
'''exonRegionColor''': The color of exon region. Can be NULL.
'''beanPlotXAxisLabelAngle''': The lable angle of bean plot x axis. Can be NULL.
'''beanPlotXAxisLableCex''': The cex of bean plot x axis. Can be NULL.
'''beanPlotXAxisLablePos1''': The position 1 of bean plot x axis lable. Can be NULL.
'''beanPlotXAxisLablePos2''': The position 2 of bean plot x axis lable. Can be NULL.
'''width''': The width of plot. Default is 14.1 . Can be NULL.
'''height''': The height of plot. Default is 10. Can be NULL.
'''format''': The format of plot. It can be pdf,tiff and png. Can be NULL.
'''outDIR''': The result directory. All intermediate files and result plot file are in this folder.
== Testing geneZoom ==
There is an example directory in ~/geneZoom. You can find vcf file, phenotype file and on sh file.
Run geneZoom example.sh.
sh ~/geneZoom/example/example.sh
After running 2 minutes +/- 1 minutes. You will get result file "PCSK9.pdf" in your defined output directory.
== Acknowledgements ==
'''geneZoom''' is the result of collaborative efforts by Cristen Willer, Jin Chen, He zhang, Ellen Schmidt, Wei Zhou, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] with any questions.
