seqc.diff.plot: seqc.diff.plot
In plger/RNAontheBENCH: RNAontheBENCH - Benchmark of RNAseq quantification and DEA

Produces a combination of 'positives plot' (see posplot) for a list of differential expression calls on the SEQC data. The x/ylim parameters control the 'zoomed plots' (on the right); the default settings are good for gene-level using all replicates. For gene-level with only 3 samples/group, use: xlim=c(0,60), ylimAB=c(5000,15500), ylimCD=c(2000,12000) For transcript-level with all samples, use: xlim=c(0,250), ylimAB=c(10000,24000), ylimCD=c(4000,17000) For transcript-level with only 3 samples/group, use: xlim=c(0,200), ylimAB=c(0,23000), ylimCD=c(0,14000) If using FDR, try the following zoom windows: gene-level (all): xlim=c(0,50),ylimAB=c(14000,21000),ylimCD=c(8000,18000) gene-level (subset): xlim=c(0,60),ylimAB=c(8000,20000),ylimCD=c(2000,17000) transcript-level (all): xlim=c(0,200), ylimAB=c(10000,35000), ylimCD=c(2000,35000) transcript-level (subset): xlim=c(0,250), ylimAB=c(0,35000), ylimCD=c(0,27000)

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seqc.diff.plot(ps, xlim = c(0, 60), ylimAB = c(8000, 17000),
  ylimCD = c(5000, 14000), use.fdr = FALSE, zoom.AUC = FALSE,
  pthreshold = 0.01, plotZoomGrid = F)

`ps`	A list with softwares as names, and lists as elements, as produced by the 'diff.seqc.example' function. Each sublist contains the results of comparisons between A vs B, C vs D, and within each group.
`xlim`	x coordinates for the zoomed plot.
`ylimAB`	y coordinates for the AvsB zoomed plot.
`ylimCD`	y coordinates for the CvsD zoomed plot.
`use.fdr`	Logical; whether to use adjust the p-values for multiple testing (FDR); default FALSE.
`zoom.AUC`	whether to report AUC for the zoomed portion of the plot.
`pthreshold`	P-value threshold, to be plotted as a point on the curve and used in the returned statistics.
`plotZoomGrid`	Logical; whether to plot the dashed square indicating, in the overall plot, the zoomed region (default false).