plotHist {facopy} | R Documentation |
The function plots a stacked histogram of chromosome arm alterations by variable value
plotHist(fad, alteration, varName, sel = NULL, selColors = NULL, selOnly = FALSE, baseColor = "black", bin = 0.05, xmax = 1, ymax)
fad |
|
alteration |
A character describing the kinds of alteration to include. It should be one of the following: |
varName |
A character indicating the variable of interest within the |
sel |
A character vector with the chromosome arms that will be highlighted using the colors in |
selColors |
A vector of colors with the same length as the parameter |
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 |
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. |
Alteration frequencies are calculated genomic feature-wise within each chromosome arm.
David Mosen-Ansorena
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)