geneplotter: Graphics related functions for Bioconductor

plotChr

R Documentation

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`.

Author(s)

Robert Gentleman and Xiaochun Li

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)

Bioconductor/geneplotter documentation built on Nov. 2, 2024, 7:25 a.m.