symbolsInteresting {XDE} | R Documentation |
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) |
Author(s)
R. Scharpf
Examples
data(expressionSetList)
data(xmcmc)
bes <- bayesianEffectSize(xmcmc)
postAvg <- posteriorAvg(xmcmc)
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)
[Package
XDE version 1.2.0
Index]