plotDispEsts: Plot Fitted and Test-wise Dispersion

In JunctionSeq: JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data

Description

Plots the countbin-specific estimated dispersion and the fitted dispersion curve.

Usage

  plotDispEsts( jscs, ylim, xlim, 
               linecol=c("#0000FF","#FF0000"), 
               pointcol = c("#00009980","#99000080"),
               title.main = "Dispersion Estimates", 
               xlab = "Mean Normalized Coverage", 
               ylab = "Dispersion",
               miniTicks = TRUE,
               pch.MLE = 46, pch.MAP = 1, lwd.fitted = 2,
               par.cex = 1, points.cex = 1, text.cex = 1, lines.cex = 8,
               use.smoothScatter = FALSE, smooth.nbin = 512, nrpoints = 100,
               plot.exon.results = TRUE, 
               plot.junction.results = TRUE, 
               anno.lwd = 2,
               mar = c(4.1,4.1,3.1,1.1),
               show.legends = TRUE, 
               verbose = TRUE, debug.mode = FALSE,
               ... )

Arguments

jscs	A JunctionSeqCountSet. Usually created by runJunctionSeqAnalyses. Alternatively, this can be created manually by readJunctionSeqCounts. Dispersions and size factors must then be set, usually using functions estimateSizeFactors and estimateJunctionSeqDispersions. Hypothesis tests must be performed by testForDiffUsage.
ylim	The plotting range for the y-axis.
xlim	The plotting range for the x-axis.
linecol	Character vector of length 2. The line color to use for the fit line. If the fits were performed separately for exons and junctions, the junction line will be drawn with the second color.
pointcol	Character vector of length 2. The point color to use for the final dispersions. If the fits were performed separately for exons and junctions, the junction points will be drawn with the second color.
title.main	The main title of the plot.
xlab	The label for the x-axis.
ylab	The label for the y-axis.
miniTicks	Whether or not to plot smaller ticks at the tenth-decades.
par.cex	The base cex value to be passed to par() immediately before all plots are created. See par.
points.cex	The character expansion value for the plotted points.
text.cex	The character expansion value for the annotation text (labels, etc).
lines.cex	The character expansion value for lines. What this means seems to vary depending on the plotting device.
pch.MLE	Numeric. The pch code for the MLE (ie single-feature) dispersion estimate. The default is a small point.
pch.MAP	Numeric. The pch code for the MAP (ie. final) dispersion estimate. The default is a circle.
lwd.fitted	Numeric. The width of the dispersion fit line(s).
use.smoothScatter	Logical. If TRUE, features will be ploted with density shading rather than having each point plotted.
smooth.nbin	The number of bins to smooth, for the density plot, if use.smoothScatter is TRUE.
nrpoints	The number of extra points to plot, if use.smoothScatter is TRUE.
plot.exon.results	Logical. If TRUE, plot results for exons. Technically speaking, JunctionSeq can be used to do DEXSeq-style analyses on exon partitions. However this functionality is for advanced users only.
plot.junction.results	Logical. If TRUE, plot results for splice junctions. For advanced users only.
anno.lwd	The lwd value to be passed to lines, box, axis, and similar.
mar	The margin sizes, expressed in lines. see link{par}.
show.legends	Logical. If TRUE, display legends.
verbose	if TRUE, send debugging and progress messages to the console / stdout.
debug.mode	if TRUE, send even more debugging and progress messages to the console / stdout.
...	Additional options to pass to plotting functions, particularly graphical parameters.

Value

This is a side-effecting function, and does not return a value.

Examples

data(exampleDataSet,package="JctSeqData");
plotDispEsts(jscs);

## Not run: 
########################################
#Set up example data:
decoder.file <- system.file(
                  "extdata/annoFiles/decoder.bySample.txt",
                  package="JctSeqData");
decoder <- read.table(decoder.file,
                  header=TRUE,
                  stringsAsFactors=FALSE);
gff.file <- system.file(
            "extdata/cts/withNovel.forJunctionSeq.gff.gz",
            package="JctSeqData");
countFiles <- system.file(paste0("extdata/cts/",
     decoder$sample.ID,
     "/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz"),
     package="JctSeqData");
######################
#Run example analysis:
jscs <- runJunctionSeqAnalyses(sample.files = countFiles,
           sample.names = decoder$sample.ID,
           condition=factor(decoder$group.ID),
           flat.gff.file = gff.file,
           analysis.type = "junctionsAndExons"
);
########################################

#Plot dispersions:
plotDispEsts(jscs);


## End(Not run)

JunctionSeq documentation built on April 28, 2020, 7:57 p.m.