Install it directly from GitHub:

library(devtools)
install_github("dakl/oncoprint")

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.