wrGraph (version 1.1.0)

MAplotW: MA-plot (differential intensity versus average intensity)

Description

This type of plot is very common in high-throughput biology, see MA-plot. Basically one would like to compare numerous independent measures (ie gene transcript or protein abundance values) of 2 samples/data-sets, it is usual to compare a change ('Minus'=M) versus absolute mean value ('Average'=A). In high-throughput biology data are typically already transformed to log2 and thus, the 'M'-value represents a relative change. Besides, output from statistical testing by moderTest2grp can be directly read to produce MA plots for diagnostic reasons. Please note, that plotting a very number of points in transparency (eg >10000) may take several seconds.

Usage

MAplotW(
  Mvalue,
  Avalue = NULL,
  filtFin = NULL,
  ProjNa = NULL,
  FCthrs = NULL,
  subTxt = NULL,
  grayIncrem = TRUE,
  compNa = NULL,
  batchFig = FALSE,
  cexMa = 1.8,
  cexLa = 0.7,
  limM = NULL,
  limA = NULL,
  cexPt = NULL,
  cexSub = NULL,
  useMar = c(6.2, 4, 4, 2),
  callFrom = "",
  silent = FALSE,
  debug = FALSE
)

Arguments

Mvalue

(numeric or matrix) data to plot; M-values are typically calculated as difference of log2-abundance values and 'Avalue' the mean of log2-abundance values; M-values and A-values may be given as 2 columsn of a matrix, in this case the argument Avalue should remain NULL

Avalue

(numeric, list or data.frame) if NULL it is assumed that 2nd column of 'Mvalue' contains the A-values to be used

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 as increased shades of gray

compNa

(character) names of groups compared

batchFig

(logical) if TRUE figure title and axes legends will be kept shorter for display on fewer splace

cexMa

(numeric) expansion factor for font-size of title (see also par)

cexLa

(numeric) expansion factor cex for labels (see also par)

limM

(numeric, length=2) range of axis M-values

limA

(numeric, length=2) range of axis A-values

cexPt

(numeric) expansion factor cex for points (see also par)

cexSub

(numeric) expansion factor cex for subtitle (see also par)

useMar

(numeric,length=4) custom margings (see also par)

callFrom

(character) allow easier tracking of message(s) produced

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

Value

MA-plot only

See Also

(for PCA) plotPCAw

Examples

# NOT RUN {
library(wrMisc)
set.seed(2005); mat <- matrix(round(runif(600),1),ncol=6)
rownames(mat) <- c(rep(letters[1:25],each=3),letters[2:26])
MAplotW(mat[,2]-mat[,1], rowMeans(mat))
## assume 2 groups with 3 samples each
matMeans <- rowGrpMeans(mat, gr=gl(2,3,labels=LETTERS[3:4]))
MAplotW(matMeans[,2]-matMeans[,1], 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) 

# }

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