TCGAbiolinks (version 1.2.5)

TCGAvisualize_oncoprint: Creating a oncoprint

Description

Creating a oncoprint

Usage

TCGAvisualize_oncoprint(mut, genes, filename, color, annotation.position = "bottom", annotation, height, rm.empty.columns = FALSE, show.column.names = FALSE, show.row.barplot = TRUE, label.title = "Mutation", label.font.size = 16, rows.font.size = 16, dist.col = 0.5, dist.row = 0.5, row.order = FALSE, heatmap.legend.side = "bottom", annotation.legend.side = "bottom")

Arguments

mut

A dataframe from the mutation annotation file (see TCGAquery_maf from TCGAbiolinks)

genes

Gene list

filename

name of the pdf

color

named vector for the plot

annotation.position

Position of the annotation "bottom" or "top"

annotation

Matrix or data frame with the annotation. Should have a column bcr_patient_barcode with the same ID of the mutation object

height

pdf height

rm.empty.columns

If there is no alteration in that sample, whether remove it on the oncoprint

show.column.names

Show column names? Default: FALSE

show.row.barplot

Show barplot annotation on rows?

label.title

Title of the label

label.font.size

Size of the fonts

rows.font.size

Size of the fonts

dist.col

distance between columns in the plot

dist.row

distance between rows in the plot

row.order

Order the genes (rows). Genes with more mutations will be in the first rows

heatmap.legend.side

Position of the heatmap legend

annotation.legend.side

Position of the annotation legend

Value

A oncoprint plot

Examples

mut <- TCGAbiolinks::TCGAquery_maf(tumor = "GBM",
       archive.name = "ucsc.edu_GBM.IlluminaGA_DNASeq_automated.Level_2.1.1.0")
TCGAvisualize_oncoprint(mut = mut, genes = mut$Hugo_Symbol[1:10], rm.empty.columns = TRUE)
TCGAvisualize_oncoprint(mut = mut, genes = mut$Hugo_Symbol[1:10],
                 filename = "onco.pdf",
                 color=c("background"="#CCCCCC","DEL"="purple","INS"="yellow","SNP"="brown"))
clin <- TCGAbiolinks::TCGAquery_clinic("gbm","clinical_patient")
clin <- clin[,c("bcr_patient_barcode","disease","gender","tumor_tissue_site","race","vital_status")]
TCGAvisualize_oncoprint(mut = mut, genes = mut$Hugo_Symbol[1:20],
                filename = "onco.pdf",
                annotation = clin,
                color=c("background"="#CCCCCC","DEL"="purple","INS"="yellow","SNP"="brown"),
                rows.font.size=10,
                heatmap.legend.side = "right",
                dist.col = 0,
                label.font.size = 10)