plotMA: Makes a so-called "MA-plot"

In DESeq: Differential gene expression analysis based on the negative binomial distribution

Description

A simple helper function that makes a so-called "MA-plot", i.e. a scatter plot of logarithmic fold changes (on the y-axis) versus the mean of normalized counts (on the x-axis).

Usage

plotMA(x, ylim,
  col = ifelse(x$padj>=0.1, "gray32", "red3"),
  linecol = "#ff000080",
  xlab = "mean of normalized counts", ylab = expression(log[2]~fold~change),
  log = "x", cex=0.45, ...)

Arguments

x	a data.frame with columns baseMean, and log2FoldChange. In addition, if the argument col is left at its default, this data.frame also needs to have a column named padj.
linecol	colour used for the horizontal line at y=0.
ylim, col, xlab, ylab, log, cex, ...	arguments that are passed on to plot.default.

Details

This is a trivial helper function. Do not be afraid to edit and modify it to your needs.

Value

The function is called for its side effect.

Author(s)

Wolfgang Huber

Examples

## see vignette

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.

DESeq documentation built on April 28, 2020, 6:37 p.m.