oncoprint's Introduction

Oncoprint

Install

Install it directly from GitHub:

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

Usage

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.

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