This package can be used to create beautiful oncoprints in R.
library(oncoprint)
data(tcga_brca)
# vertical x-labels
vert_x <- theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust=.5))
oncoprint(tcga_brca) + coord_fixed() + vert_x
The main function (oncoprint(M)) works on a matrix of strings on on this form:
TCGA-BH-A1EV-01 TCGA-A2-A1FW-01 TCGA-AO-A1KS-01 TCGA-D8-A1JB-01 TCGA-D8-A1JD-01
BRCA1 "" "" "" "" ""
BRCA2 "AMP;" "AMP;" "AMP;" "HOMDEL;" "HOMDEL;"
Row names are genes, column names are samples. The following annotations are allowed by default:
- Ampilifications (
AMP), red fill - Deletions (
HOMDEL), blue fill - Somatic mutations (
MUT), green box - Germline mutations (
GERMLINE), purple box - Upregulation (
UP), red outline - Downregulation (
DOWN), blue outline
Each element is changable by passing (defaults listed below)
keys = list(somatic = "MUT", germline = "GERMLINE", amp = "AMP",
del = "HOMDEL", upreg = "UP", downreg = "DOWN")
to the function call. Also, the genes can be sorted by most altered gene by passing sortGenes = TRUE (default FALSE, which keeps order from matrix). Samples are always sorted using an adaptation of the algorithm used in cBioPortal.