facopy (version 1.6.0)

plotBar: Overview of Alterations by Chromosome Arm

Description

The function plots amplification and deletion frequencies by chromosome arm, as well as LOH frequencies

Usage

plotBar(fad, byFeature = TRUE, sel = NULL, selColors = NULL,  ylim = c(-1, 1), baseColor = "black",  varName = NULL, value = NULL)

Arguments

fad

facopyInfo object with a certain study's facopy data.

byFeature

A logical. If TRUE, arm frequencies are calculated as the mean alteration frequencies across genomic features in each arm. If TRUE, they are calculated as the mean proportion of altered base pairs in each arm.

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.

ylim

A two integer vector indicating frequency limits in the plot. Deletion frequency is indicated with a negative number. Default is c(-1,1).

baseColor

Base color of the triangles that indicate frequencies in the plot. Default is "black".

varName

Either NULL or a character indicating the variable of interest within the facopyInfo object. Call summary on your facopyInfo object to see the names of defined variables. If NULL, the frequencies across all samples are plotted. Otherwise, only samples with the variable value in the parameter value are selected for the computation. In this latter case, only categorical variables are allowed.

value

Value that the samples should have for the selected variable. Only these samples are selected for the frequency calculation.

Details

Amplification frequencies are depicted by chromosome arm over the horizontal line, while deletion frequencies appear below it. The frequencies of alterations with LOH are depicted as smaller triangles.

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])

plotBar(myStudy, TRUE, myArms, myColors, ylim=c(-0.5,1))