TCGAvisualize_oncoprint {TCGAbiolinks} | R Documentation |
Creating a oncoprint
TCGAvisualize_oncoprint(mut, genes, filename, color, annotation.position = "bottom", annotation, height, width = 10, rm.empty.columns = FALSE, show.column.names = FALSE, show.row.barplot = TRUE, label.title = "Mutation", column.names.size = 8, label.font.size = 16, rows.font.size = 16, dist.col = 0.5, dist.row = 0.5, information = "Variant_Type", row.order = TRUE, col.order = TRUE, heatmap.legend.side = "bottom", annotation.legend.side = "bottom")
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 |
width |
pdf width |
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 |
column.names.size |
Size of the fonts of the columns names |
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 |
information |
Which column to use as informastion from MAF. Options: 1) "Variant_Classification" (The information will be "Frame_Shift_Del", "Frame_Shift_Ins", "In_Frame_Del", "In_Frame_Ins", "Missense_Mutation", "Nonsense_Mutation", "Nonstop_Mutation", "RNA", "Silent" , "Splice_Site", "Targeted_Region", "Translation_Start_Site") 2) "Variant_Type" (The information will be INS,DEL,SNP) |
row.order |
Order the genes (rows) Default:TRUE. Genes with more mutations will be in the first rows |
col.order |
Order columns. Default:TRUE. |
heatmap.legend.side |
Position of the heatmap legend |
annotation.legend.side |
Position of the annotation legend |
A oncoprint plot
## Not run: mut <- GDCquery_Maf(tumor = "ACC", pipelines = "mutect") 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 <- GDCquery_clinic("TCGA-ACC","clinical") clin <- clin[,c("bcr_patient_barcode","disease","gender","tumor_stage","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) ## End(Not run)