plotMA {JunctionSeq} | R Documentation |
Generates an MA-plot, which graphs the fold change versus the mean normalized expression. Statistically significant features are colored red.
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, ...)
jscs |
A Alternatively, this can be created manually by |
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 |
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 |
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 |
points.cex |
The cex value to be passed to |
text.cex |
The cex value to be passed to |
lines.cex |
|
anno.lwd |
The lwd value to be passed to |
mar |
The margin sizes, expressed in lines. see |
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. |
This is a side-effecting function, and does not return a value.
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)