Usage: phewas_view.rb | |
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Standard PheWAS Plot | |
-v, --version | Show PheWAS-View version |
-e phewas file | PheWAS-View formatted file for input |
-o output name | Optional output name for the resultant plot |
-t title | Main title for the plot (enclose in quotes) |
-f image type | Image format for output (png default). Other options depend on ImageMagick installation. |
-w, --lowres | Low resolution image (72 dpi) |
-a, --rotate | Rotate final image 90 degrees |
-p p-value threshold | p-value threshold, values less significant will be plotted in grey |
-m, --maxp maximum p-value | Maximum p-value to plot. Values less significant than the specified cut off are not plotted |
-R, --redline p-value | Draw a red line at the designated p-value |
-b | Include direction of effect on plot |
-A, --samp-size | Include sample size plot |
-l ancestry map file | Optional ancestry map file |
-c phenotype class names | Only results matching this phenotype class name are plotted |
-B, --showbest | Display detailed information for best score at each phenotype |
-x phenotype/SNP file | PheWAS expected SNP/phenotype file |
-r ancestry | List of race/ethnicities to include (AA, EA, MA) |
-s SNP ID | SNP ID to display from input file |
-L phenotype list file | Optional phenotype list for inclusion |
-N, --no-lines | No background lines drawn on plot |
-C phenotype correlation file | Optional file with phenotype correlations |
Sun Plot Settings | |
-S | Produce sun plot |
-s SNP ID | SNP ID to display in center of sun plot |
-P phenotype name | Phenotype to display in center of sun plot |
-g gene name | Gene to display in center of sun plot |
-G | Include gene name along with SNP, when SNP is selected for sun plot |
-E | Include ancestry as description of result for sun plot |
-m, --maxp p-value | Choose a p-value threshold, p-values less significant will not be plotted |
-p p-value | For plotted results, any results more significant will be plotted in red |
-b | To apply direction of effect for phenotypes in sun plot, - is negative direction, + is positive direction |