plotChr {geneplotter} | 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

### 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)

[Package geneplotter version 1.22.0 Index]