Description Usage Arguments Examples
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.
1 2 | saveERCCPlots(exDat, plotsPerPg = "main", saveas = "pdf", outName, plotlist,
res)
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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 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | 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))
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