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);

    ## 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)

[Package JunctionSeq version 1.12.1 Index]