wrGraph: MAplotW – R documentation

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MAplotW

MA-plot (differential intensity versus average intensity)

Description

This type of plot for display of relative changes versus (mean) absolute abundance is very common in high-throughput biology, see MA-plot. Basically one compares two independent series of measures (ie gene transcript or protein abundance values) of 2 samples/data-sets or the means of 2 groups of replicates. And the log-fold-change ('Minus'=M) is plotted againts the absolute mean value ('Average'=A). Furthermore, output from statistical testing by moderTest2grp or moderTestXgrp can be directly read to produce MA plots for diagnostic purpose. Please note, that plotting a very high number of points in transparency (eg >10000) may take several seconds.

Usage

MAplotW(
  Mvalue,
  Avalue = NULL,
  useComp = 1,
  filtFin = NULL,
  ProjNa = NULL,
  FCthrs = NULL,
  subTxt = NULL,
  grayIncrem = TRUE,
  col = NULL,
  pch = 16,
  compNa = NULL,
  batchFig = FALSE,
  cexMa = 1.8,
  cexLa = 1.1,
  limM = NULL,
  limA = NULL,
  annotColumn = c("SpecType", "GeneName", "EntryName", "Accession", "Species",
    "Contam"),
  annColor = NULL,
  cexPt = NULL,
  cexSub = NULL,
  cexTxLab = 0.7,
  namesNBest = NULL,
  NbestCol = 1,
  NaSpecTypeAsContam = TRUE,
  useMar = c(6.2, 4, 4, 2),
  returnData = FALSE,
  callFrom = NULL,
  silent = FALSE,
  debug = FALSE
)

Arguments

`Mvalue`	(numeric, list or MArrayLM-object) main data to plot; if numeric, the content will be used as M-values (and A-values must be provided separateley); if list or MArrayLM-object, it must conatin list-elements named `Mvalue` and `means` to extract all information needed for plotting
`Avalue`	(numeric, list or data.frame) if `NULL` it is assumed that M-values can be extracted form argument `Avalue`
`useComp`	(integer) choice of one of multiple comparisons present in `Mvalue` (if generated using `moderTestXgrp()`)
`filtFin`	(matrix or logical) The data may get filtered before plotting: If `FALSE` no filtering will get applied; if matrix of `TRUE`/`FALSE` it will be used as optional custom filter, otherwise (if `Mvalue` if an `MArrayLM`-object eg from limma) a default filtering based on the `filtFin` element will be applied
`ProjNa`	(character) custom title
`FCthrs`	(numeric) Fold-Change threshold (display as line) give as Fold-change and NOT log2(FC)
`subTxt`	(character) custom sub-title
`grayIncrem`	(logical) if `TRUE`, display overlay of points (not exceeding threshold) as increased shades of gray
`col`	(character) custom color(s) for points of plot (see also `par`)
`pch`	(integer) type of symbol(s) to plot (default=16) (see also `par`)
`compNa`	depreciated, please use `useComp` instead
`batchFig`	(logical) if `TRUE` figure title and axes legends will be kept shorter for display on fewer splace
`cexMa`	(numeric) font-size of title, as expansion factor (see also `cex` in `par`)
`cexLa`	(numeric) size of axis-labels, as expansion factor (see also `cex` in `par`)
`limM`	(numeric, length=2) range of axis M-values
`limA`	(numeric, length=2) range of axis A-values
`annotColumn`	(character) column names of annotation to be extracted (only if `Mvalue` is `MArrayLM`-object containing matrix $annot). The first entry (typically 'SpecType') is used for different symbols in figure, the second (typically 'GeneName') is used as prefered text for annotating the best points (if `namesNBest` allows to do so.)
`annColor`	(character or integer) colors for specific groups of annotation (only if `Mvalue` is `MArrayLM`-object containing matrix $annot)
`cexPt`	(numeric) size of points, as expansion factor (see also `cex` in `par`)
`cexSub`	(numeric) size of subtitle, as expansion factor (see also `cex` in `par`)
`cexTxLab`	(numeric) size of text-labels for points, as expansion factor (see also `cex` in `par`)
`namesNBest`	(integer or character, length=1) number of best points to add names in figure; if 'passThr' all points passing FC-filter will be selected; if the initial object `Mvalue` contains a list-element called 'annot' the second of the column specified in argument `annotColumn` will be used as text
`NbestCol`	(character or integer) colors for text-labels of best points
`NaSpecTypeAsContam`	(logical) consider lines/proteins with `NA` in Mvalue$annot[,"SpecType"] as contaminants (if a 'SpecType' for contaminants already exits)
`useMar`	(numeric,length=4) custom margings (see also `par`)
`returnData`	(logical) optional returning data.frame with (ID, Mvalue, Avalue, FDRvalue, passFilt)
`callFrom`	(character) allow easier tracking of message(s) produced
`silent`	(logical) suppress messages
`debug`	(logical) additional messages for debugging

Value

MA-plot only

Examples

library(wrMisc)
set.seed(2005); mat <- matrix(round(runif(600),2), ncol=6)
rownames(mat) <- c(rep(letters[1:25],each=3), letters[2:26])
MAplotW(mat[,2] -mat[,1], A=rowMeans(mat))
## assume 2 groups with 3 samples each
matMeans <- rowGrpMeans(mat, gr=gl(2,3,labels=LETTERS[3:4]))
MAplotW(M=matMeans[,2] -matMeans[,1], A=matMeans) 
## assume 2 groups with 3 samples each and run moderated t-test (from package 'limma')
tRes <- moderTest2grp(mat, gl(2,3))
MAplotW(tRes$Mval, tRes$Amean)                          
MAplotW(M=tRes$Mval, A=tRes$means, FCth=1.3) 
MAplotW(tRes)
MAplotW(tRes, limM=c(-2,2), FCth=1.3)

wrGraph

Graphics in the Context of Analyzing High-Throughput Data

v1.2.3

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release