wrProteo: VolcanoPlotW2 – R documentation

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VolcanoPlotW2

Volcano-plot (Statistical Test Outcome versus Relative Change)

Description

This type of plot is very common in high-throughput biology, see Volcano-plot. Basically, this plot allows comparing the outcome of a statistical test to the differential of the group means (ie log fold-change),

Usage

VolcanoPlotW2(
  Mvalue,
  pValue = NULL,
  useComp = 1,
  filtFin = NULL,
  ProjNa = NULL,
  FCthrs = NULL,
  FdrList = NULL,
  FdrThrs = NULL,
  FdrType = NULL,
  subTxt = NULL,
  grayIncrem = TRUE,
  col = NULL,
  pch = 16,
  compNa = NULL,
  batchFig = FALSE,
  cexMa = 1.8,
  cexLa = 1.1,
  limM = NULL,
  limp = NULL,
  annotColumn = c("SpecType", "GeneName", "EntryName", "Accession", "Species",
    "Contam"),
  annColor = NULL,
  cexPt = NULL,
  cexSub = NULL,
  cexTxLab = 0.7,
  namesNBest = NULL,
  NbestCol = 1,
  sortLeg = "descend",
  NaSpecTypeAsContam = TRUE,
  useMar = c(6.2, 4, 4, 2),
  returnData = FALSE,
  callFrom = NULL,
  silent = FALSE,
  debug = FALSE
)

Arguments

`Mvalue`	(numeric or matrix) data to plot; M-values are typically calculated as difference of log2-abundance values and 'pValue' the mean of log2-abundance values; M-values and p-values may be given as 2 columsn of a matrix, in this case the argument `pValue` should remain NULL
`pValue`	(numeric, list or data.frame) if `NULL` it is assumed that 2nd column of 'Mvalue' contains the p-values to be used
`useComp`	(integer, length=1) choice of which of multiple comparisons to 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), default at 1.5, set to `NA` for omitting
`FdrList`	(numeric) FDR data or name of list-element
`FdrThrs`	(numeric) FDR threshold (display as line), default at 0.05, set to `NA` for omitting
`FdrType`	(character) FDR-type to extract if `Mvalue` is 'MArrayLM'-object (eg produced by from `moderTest2grp` etc); if `NULL` it will search for suitable fields/values in this order : 'FDR','BH',"lfdr" and 'BY'
`subTxt`	(character) custom sub-title
`grayIncrem`	(logical) if `TRUE`, display overlay of points 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`	(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) 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
`limp`	(numeric, length=2) range of axis FDR / p-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 annoatation (only if `Mvalue` is `MArrayLM`-object containing matrix $annot)
`cexPt`	(numeric) size of points, as expansion factor (see also `cex` in `par`)
`cexSub`	(numeric) size of subtitle, as expansion factor (see also `cex` in `par`)
`cexTxLab`	(numeric) size of text-labels for points, as expansion factor (see also `cex` in `par`)
`namesNBest`	(integer or character) number of best points to add names in figure; if 'passThr' all points passing FDR and FC-filtes will be selected; if the initial object `Mvalue` contains a list-element called 'annot' the second of the column specified in argument `annotColumn` will be used as text
`NbestCol`	(character or integer) colors for text-labels of best points
`sortLeg`	(character) sorting of 'SpecType' annotation either ascending ('ascend') or descending ('descend'), no sorting if `NULL`
`NaSpecTypeAsContam`	(logical) consider lines/proteins with `NA` in Mvalue$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, pValue, FDRvalue, passFilt)
`callFrom`	(character) allow easier tracking of message(s) produced
`silent`	(logical) suppress messages
`debug`	(logical) additional messages for debugging

Details

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 or moderTestXgrp can be directly read to produce Volcano plots for diagnostic reasons. Please note, that plotting a very number of points in transparency (eg >10000) may take several seconds.

Value

MA-plot only

Examples

library(wrMisc)
set.seed(2005); mat <- matrix(round(runif(900),2), ncol=9)
rownames(mat) <- paste0(rep(letters[1:25],each=4), rep(letters[2:26],4))
mat[1:50,4:6] <- mat[1:50,4:6] + rep(c(-1,1)*0.1,25)
mat[3:7,4:9] <- mat[3:7,4:9] + 0.7
mat[11:15,1:6] <- mat[11:15,1:6] - 0.7
## assume 2 groups with 3 samples each
gr3 <- gl(3,3,labels=c("C","A","B"))
tRes2 <- moderTest2grp(mat[,1:6], gl(2,3), addResults = c("FDR","means"))
## Please NOTE : the function VolcanoPlotW2 has been depreaciated, 
## please use VolcanoPlotW() from package wrGraph
library(wrGraph)
VolcanoPlotW(tRes2)

wrProteo

Proteomics Data Analysis Functions

v1.4.1

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release