gisticBubblePlot {maftools} | R Documentation |
Plots significantly altered cytobands as a function of number samples in which it is altered and number genes it contains. Size of each bubble is according to -log10 transformed q values.
gisticBubblePlot(gistic = NULL, color = NULL, markBands = NULL, fdrCutOff = 0.1, txtSize = 3, file = NULL, width = 6, height = 5)
gistic |
an object of class |
color |
colors for Amp and Del events. |
markBands |
any cytobands to label. |
fdrCutOff |
fdr cutoff to use. Default 0.1 |
txtSize |
label size for bubbles. |
file |
if given saves plot as a pdf. |
width |
width of the file to be saved. |
height |
height of the file to be saved. |
invisible ggplot2 object
all.lesions <- system.file("extdata", "all_lesions.conf_99.txt", package = "maftools") amp.genes <- system.file("extdata", "amp_genes.conf_99.txt", package = "maftools") del.genes <- system.file("extdata", "del_genes.conf_99.txt", package = "maftools") scores.gistic <- system.file("extdata", "scores.gistic", package = "maftools") laml.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, gisticDelGenesFile = del.genes, gisticScoresFile = scores.gistic) gisticBubblePlot(gistic = laml.gistic)