QQPLOT - winkusch/Easy2 GitHub Wiki
Create QQ plot.
| FUNCTION | PARAMETER | DEFAULT | DESCRIPTION |
|---|---|---|---|
| QQPLOT | --acolQQPlot | array of columns to be drawn in QQ plot (eg P value columns) | |
| QQPLOT | --astrColour | black | array of colours according to criteria |
| QQPLOT | --anumSymbol | 20 | array of symbol values (R's pch parameter) |
| QQPLOT | --anumCex | 1 | array of symbol sizes (R's cex parameter) |
| QQPLOT | --blnCombined | FALSE | |
| QQPLOT | --blnLegend | FALSE | logical whether legend should be added |
| QQPLOT | --astrLegendText | ||
| QQPLOT | --strMode | singleplot | plot mode (singleplot or subplot) |
| QQPLOT | --arcdExclude | array of R expressions according to with values will be excluded | |
| QQPLOT | --arcdInclude | array of R expression according to with values will be included | |
| QQPLOT | --numPvalOffset | 1 | |
| QQPLOT | --strAxes | ||
| QQPLOT | --strXlab | Plot x axis label | |
| QQPLOT | --strYlab | Plot y axis label | |
| QQPLOT | --strTitle | Plot title | |
| QQPLOT | --arcdAdd2Plot | array of R code expressions that will be added to the plot (eg text(…)) | |
| QQPLOT | --strFormat | png | graphic file format |
| QQPLOT | --numCexAxis | 1 | cex for axis |
| QQPLOT | --numCexLab | 1 | cex for lables |
| QQPLOT | --numWidth | 640, | Width of the plot in pixel. |
| QQPLOT | --numHeight | 640, | Height of the plot in pixel. |
| QQPLOT | --anumParMar | c(5.1,4.1,4.1,2.1) | array of four 'par' parameters |
| QQPLOT | --anumParMgp | c(3,1,0) | array of three 'mgp' parameters |
| QQPLOT | --strParBty | o | plot param 'bty' |
| QQPLOT | --strPlotName | plot name (added to file name to indicate this plot) | |
| QQPLOT | --blnYAxisBreak | FALSE | logical whether y axis should be broken at certain value |
| QQPLOT | --numYAxisBreak | 22 | |
| QQPLOT | --blnLogPval | FALSE | is P value logarithmized? |
| QQPLOT | --blnPlotCI | FALSE | logical whether confidence interval should be added |
| QQPLOT | --fileRemove | ||
| QQPLOT | --numRemovePosLim | 500000 | |
| QQPLOT | --strRemovedColour | green | |
| QQPLOT | --numRemovedSymbol | 20 | |
| QQPLOT | --numRemovedCex | 1 | |
| QQPLOT | --colInChr | Column name of the input chromosome. | |
| QQPLOT | --colInPos | Column name of the input position column. | |
| QQPLOT | --blnAddLambdaGC | FALSE | logical whether GC lambda should be calculated and added to QQPLOT |
| QQPLOT | --anumChiSqDf | -1 | array of chi-squared columns |
Example:
QQPLOT --acolQQPlot Pmen;Pwomen
--astrColour blue;red
--anumSymbol 0;1
--numPvalOffset 0.05