JunctionSeq (version 1.2.4)

plotMA: 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);


## 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)