plotHist {facopy} | R Documentation

## Stacked Histograms

### Description

The function plots a stacked histogram of chromosome arm alterations by variable value

### Usage

    plotHist(fad, alteration, varName,
             sel = NULL, selColors = NULL, selOnly = FALSE,
             baseColor = "black", bin = 0.05, xmax = 1, ymax)

### Arguments

`fad` | `facopyInfo` object with a certain study's `facopy` data.
`alteration` | A character describing the kinds of alteration to include. It should be one of the following: - `amplifications` All amplifications (CN>2). - `deletions` All deletions (CN<2). - `loh` All loss of heterozygosity (LOH), regardless of copy number. - `cnas` All copy number alterations (CN<>2). - `any` Any kind of alteration. - `all` Any kind of alteration, same as `any`. - `onlygain` Only non-LOH amplifications. - `someloss` All deletions plus LOH alterations.
`varName` | A character indicating the variable of interest within the `facopyInfo` object. A stacked histogram will be generated for every value of the variable. Only available for discrete variables. Call `summary` on your `facopyInfo` object to see the names of defined variables.
`sel` | A character vector with the chromosome arms that will be highlighted using the colors in `selColors`. Example: `c("1q","9p")`.
`selColors` | A vector of colors with the same length as the parameter `sel`. Each color in the vector will be used for the selected chromosome arm in the same position within `sel`.
`selOnly` | A logical indicating whether to only plot the frequencies of selected chromosome arms.
`baseColor` | Base color of the triangles that indicate frequencies in the plot. Default is `"black"`.
`bin` | The width of the histogram cells. Default is 0.05.
`xmax` | The maximum limit of the x axis in the plot. Default is 1.
`ymax` | The maximum limit of the y axis in the plot.

### Details

Alteration frequencies are calculated genomic feature-wise within each chromosome arm.

### Author(s)

David Mosen-Ansorena

### Examples

    data(myStudy) # load example study

    # select some chromosome arms to highlight
    myArms = c("8q","13q","20q","8p","18q")
    myColors = c(rainbow(15)[1:3], rainbow(15)[10:11])

    plotHist(myStudy, "amp", "stage", myArms, myColors, bin=0.1, ymax=80)

[Package facopy version 1.13.0 Index]