saveERCCPlots {erccdashboard} | R Documentation |
The function savePlots will save selected figures to a pdf file. The default is the 4 manuscript figures to a single page (plotsPerPg = "manuscript"). If plotsPerPg = "single" then each plot is placed on an individual page. If plotlist is not defined (plotlist = NULL) or if plotlist = exDat$Figures then all plots in exDat$Figures are printed to a PDF file.
saveERCCPlots(exDat, plotsPerPg = "main", saveas = "pdf", outName, plotlist, res)
exDat |
list, contains input data and stores analysis results |
plotsPerPg |
string, if "main" then the 4 main plots are printed to one page, if "single" then a single plot is printed per page from the plotlist argument |
saveas |
Choose file format from "pdf", "jpeg" or "png" |
outName |
Choose output file name, default will be fileName from exDat |
plotlist |
list, contains plots to print |
res |
Choose the file resolution |
data(SEQC.Example) exDat <- initDat(datType="count", isNorm=FALSE, exTable=MET.CTL.countDat, filenameRoot="testRun", sample1Name="MET", sample2Name="CTL", erccmix="RatioPair", erccdilution=1/100, spikeVol=1, totalRNAmass=0.500, choseFDR=0.1) exDat <- est_r_m(exDat) exDat <- dynRangePlot(exDat) exDat <- geneExprTest(exDat) exDat <- erccROC(exDat) exDat <- estLODR(exDat, kind="ERCC", prob=0.9) exDat <- annotLODR(exDat) #to print 4 main plots to a single page pdf file saveERCCPlots(exDat, plotsPerPg = "manuscript",saveas = "pdf") #to print 4 plots to a jpeg file saveERCCPlots(exDat, plotsPerPg = "manuscript",saveas = "jpeg") # or to create a multiple page pdf of all plots produced saveERCCPlots(exDat, plotsPerPg = "single", plotlist = exDat$Figures) # or to create a multiple page pdf of just 2 plots saveERCCPlots(exDat, plotsPerPg = "single", plotlist = list(exDat$Figures$lodrPlot, exDat$Figures$maPlot))