R: Generate a MA-Plot

plotMA {JunctionSeq}

R Documentation

Generate a MA-Plot

Description

Generates an MA-plot, which graphs the fold change versus the mean normalized expression. Statistically significant features are colored red.

Usage

plotMA(jscs, 
       FDR.threshold = 0.01, 
       fc.name = NULL,
       fc.thresh = 1,
       use.pch = 20,
       smooth.nbin = 256, 
       ylim = c( 1 / 1000,1000),
       use.smoothScatter = TRUE,
       label.counts = TRUE,
       label.axes = c(TRUE,TRUE,FALSE,FALSE), 
       show.labels = TRUE,
       par.cex = 1, points.cex = 1, text.cex = 1,
       lines.cex = 8,
       anno.lwd = 2, mar = c(4.1,4.1,3.1,1.1),
       miniTicks = TRUE, 
       verbose = TRUE, debug.mode = FALSE,
       ...)

Arguments

`jscs`	A `JunctionSeqCountSet`. Usually created by `runJunctionSeqAnalyses`. Alternatively, this can be created manually by `readJunctionSeqCounts`. However in this case a number of additional steps will be necessary: Dispersions and size factors must then be set, usually using functions `estimateSizeFactors` and `estimateJunctionSeqDispersions`. Hypothesis tests must be performed by `testForDiffUsage`. Effect sizes and parameter estimates must be created via `estimateEffectSizes`.
`FDR.threshold`	The FDR threshold used to color dots. Tests with an adjusted-p-value more significant than this threshold will be marked in red.
`fc.name`	The name of the column to take from fData(jscs).
`fc.thresh`	The fold-change threshold required to count a significant locus in the count labels. It will also draw horizontal lines at this threshold.
`use.pch`	The value of pch to pass to the `points` call.
`use.smoothScatter`	Logical. If TRUE, non-significant genes will be ploted with density shading.
`smooth.nbin`	The number of bins to smooth, for the density plot, if `use.smoothScatter` is TRUE.
`ylim`	The y-axis limits.
`label.counts`	Logical. If TRUE, include labels showing the number of loci that pass both the statistical-significance and fold-change threshold in each direction.
`label.axes`	Logical vector. Whether to label each axis. Must have length 4; each corresponds to the bottom, left, top, and right axes respectively.
`show.labels`	Logical. If TRUE, include all titles and axes labels.
`par.cex`	The cex value to be passed to `par`.
`points.cex`	The cex value to be passed to `points`.
`text.cex`	The cex value to be passed to `text`.
`lines.cex`	The cex value to be passed to `lines`, `box`, and similar.
`anno.lwd`	The lwd value to be passed to `lines`, `box`, `axis`, and similar.
`mar`	The margin sizes, expressed in lines. see `link{par}`.
`miniTicks`	Logical. If TRUE, then include "mini tick marks" on the x and y axes.
`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 graphical parameters.

Value

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

Examples

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

plot of chunk unnamed-chunk-1

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

[Package JunctionSeq version 1.5.4 Index]