XDE (version 2.18.0)

symbolsInteresting: Useful for changing the look of pairs plots to emphasize concordant or discordant genes

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)

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)