plotChr {geneplotter} | R Documentation |
For a given chromosome, plot the smooths of the sense and the anti-sense from 5' to 3' (left to right on x-axis).
plotChr(chrN, senseObj, cols = rep("blue", length(senseObj[[1]])), log = FALSE, xloc = c("equispaced", "physical"), geneSymbols = FALSE, ngenes = 20, lines.at = NULL, lines.col = "red")
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 . |
Robert Gentleman and Xiaochun Li
example(Makesense) op <- par(ask=TRUE) cols <- c("red", "green")[unclass(eset133a$cov1)] 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) par(op)