TCGAvisualize_oncoprint {TCGAbiolinks} | R Documentation

## Creating a oncoprint

### Description

Creating a oncoprint

### Usage

    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"
    )

### 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
`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 information 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

### Value

A oncoprint plot

### Examples

    ## 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)

[Package TCGAbiolinks version 2.22.4 Index]