plotMA {INSPEcT} | R Documentation |
Visualize the comparison between the rates calculated from two different INSPEcT objects profiled in steady-state conditions.
## S4 method for signature 'INSPEcT_diffsteady' plotMA(object, ...)
object |
An object of calss INSPEcT_diffsteady |
... |
Additional parameters, see Details section |
Possible arguments to "plotMA":
"rate" - A character, which represent the rate to be visualized, either "synthesis", "processing" or "degradation". By default, "synthesis" is chosen.
"padj" - A numeric, The p-adjusted threshold for significance. Genes with p-adjusted lower than the threshold will be depicted as orange triangles. By default set to -Inf, meaning that no genes will be highlighted.
"xlim" - A numeric vector of length 2, limits of x-axis, by default the range of the data.
"xlab" - A character, the label of x-axis, by default "log2 geometric mean"
"ylim" - A numeric vector of length 2, limits of y-axis, by default the range of the data.
"ylab" - A character, the label of y-axis, by default "log2 fold change"
"main" - A character, the title of the plot, by default the name of the visualized rate.
http://en.wikipedia.org/wiki/MA_plot
if( Sys.info()["sysname"] != "Windows" ) { data('allcounts', package='INSPEcT') data('featureWidths', package='INSPEcT') data('libsizes', package='INSPEcT') nascentCounts<-allcounts$nascent matureCounts<-allcounts$mature conditions<-letters[1:11] expDes<-rep(conditions,3) tL<-1/6 nasExp_DESeq2<-quantifyExpressionsFromTrCounts( allcounts=nascentCounts ,libsize=nascentLS ,exonsWidths=exWdths ,intronsWidths=intWdths ,experimentalDesign=expDes) matExp_DESeq2<-quantifyExpressionsFromTrCounts( allcounts=matureCounts ,libsize=totalLS ,exonsWidths=exWdths ,intronsWidths=intWdths ,experimentalDesign=expDes) nasFullObj <- newINSPEcT(tpts=conditions ,labeling_time=tL ,nascentExpressions=nasExp_DESeq2 ,matureExpressions=matExp_DESeq2) diffrates = compareSteady(nasFullObj[,c(1,11)]) plotMA(diffrates, padj=.01) }