saveERCCPlots: Save erccdashboard plots to a pdf file

In erccdashboard: Assess Differential Gene Expression Experiments with ERCC Controls

Description

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.

Usage

saveERCCPlots(exDat, plotsPerPg = "main", saveas = "pdf", outName, plotlist,
  res)

Arguments

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

Examples

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))

erccdashboard documentation built on Nov. 8, 2020, 5:50 p.m.