symbolsInteresting: Useful for changing the look of pairs plots to emphasize...

In XDE: XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

Description

This function can be used to order genes in a matrix by the rank of a statistic and provide different plotting symbols and colors for genes that exceed a certain threshold of the ranking statistic.

Usage

symbolsInteresting(rankingStatistic, percentile = 0.9,
                   colors = c("grey50", "royalblue"),
                   symbols = c(".", "o"), size = c(3, 1),
                   background = c("white", "grey70"))

Arguments

rankingStatistic	Any numerical vector
percentile	A percentile of the rankingStatistic – above which a gene would be classified as 'interesting'
colors	character string of length 2: a color for genes not exceeding the percentile and a color for genes exceeding the thresold
symbols	two plotting symbols (numeric or character): symbol for genes not exceeding percentile and symbol for genes exceeding percentile
size	numeric vector of length 2: size of plotting symbol for genes not exceeding percentile and size of plotting symbol for genes exceeding percentile
background	character vector of length 2: background color of plotting symbols for gene not exceeding percentile and for genes exceeding the percentile

Value

order	the order of the rankingStatistic
pch	plotting symbols (same length as rankingStatistic)
col	color of plotting symbols (same length as rankingStatistic)
bg	background color of plotting symbols (same length as rankingStatistic)
cex	size of plotting symbols (same length as rankingStatistic)

Author(s)

R. Scharpf

Examples

  data(expressionSetList)
  data(xmcmc)
  pathToLogFiles <- system.file("logFiles", package="XDE")
  load(file.path(pathToLogFiles, "BES.rda"))
  load(file.path(pathToLogFiles, "postAvg.rda"))
  op.conc <- symbolsInteresting(rankingStatistic=postAvg[, "concordant"])
  graphics:::pairs(BES[op.conc$order, ], pch=op.conc$pch, col=op.conc$col, 
                   bg=op.conc$bg, upper.panel=NULL, cex=op.conc$cex)  

XDE documentation built on Nov. 8, 2020, 5:02 p.m.