plotMA: Generate a MA-Plot

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

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);


## 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 M-A:
plotMA(jscs);


## End(Not run)

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