plotBar {facopy} | R Documentation |
The function plots amplification and deletion frequencies by chromosome arm, as well as LOH frequencies
plotBar(fad, byFeature = TRUE, sel = NULL, selColors = NULL, ylim = c(-1, 1), baseColor = "black", varName = NULL, value = NULL)
fad |
|
byFeature |
A logical. If |
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 |
ylim |
A two integer vector indicating frequency limits in the plot. Deletion frequency is indicated with a negative number. Default is |
baseColor |
Base color of the triangles that indicate frequencies in the plot. Default is |
varName |
Either |
value |
Value that the samples should have for the selected variable. Only these samples are selected for the frequency calculation. |
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.
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]) plotBar(myStudy, TRUE, myArms, myColors, ylim=c(-0.5,1))