geneplotter (version 1.50.0)

plotChr: Plot Smoothed Sense/Anti-sense of Specified Chromosomes

Description

For a given chromosome, plot the smooths of the sense and the anti-sense from 5' to 3' (left to right on x-axis).

Usage

plotChr(chrN, senseObj, cols = rep("black", length(senseObj[[1]])), log = FALSE, xloc = c("equispaced", "physical"), geneSymbols = FALSE, ngenes = 20, lines.at = NULL, lines.col = "red")

Arguments

chrN

The desired chromosome, e.g. for humans it would be a character string in the set of c(1:22, "X", "Y").

senseObj

The result of Makesense.

cols

A vector of colors for the lines in the plot, typically specified according to a certain pheotype of samples.

log

Logical, whether log-transformation should be taken on the smoothed expressions.

xloc

Determines whether the "Representative Genes" will be displayed according to their relative positions on the chromosome (physical), or spaced evenly (equispaced). Default is equispaced.

geneSymbols

Logical, whether to use Affy IDs or Gene Symbols for "Representative Genes", default is Affy IDs.

ngenes

Desired number of "Representative Genes". The number of actual displayed genes may differ.

lines.at

A vector of Affy IDs. Vertical lines will be drawn at specified genes.

lines.col

A vector of colors associated with lines.at.

See Also

Makesense

Examples

example(Makesense)

if (interactive())
  op <- par(ask=TRUE)

cols <- ifelse(expressionSet133a$cov1=="test 1", "red", "green")
plotChr("21", esetobj, cols)

# plot on log-scale:

plotChr("21", esetobj, cols, log=TRUE)

# genesymbol instead of probe names:

plotChr("21", esetobj, cols, log=TRUE, geneSymbols=TRUE)

# add vertical lines at genes of interest:

gs <- c("220372_at", "35776_at", "200943_at")
plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs)

# add vertical lines at genes of interest
# with specified colors:

gs <- c("220372_at", "35776_at", "200943_at")
cc <- c("blue", "cyan","magenta")
plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs,
lines.col=cc)
if (interactive())
  par(op)