plot_recurrent_genes: Function to plot recurrent fused genes

In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Function to plot recurrent fused genes

Description

Function to plot recurrent fused genes

Usage

plot_recurrent_genes(
  standardFusioncalls,
  groupby,
  plotn = 20,
  countID,
  palette_rec = NULL,
  base_size = 20
)

Arguments

standardFusioncalls	A dataframe from star fusion or arriba standardized to run through the filtering steps
groupby	column name with grouping variables
plotn	top n recurrent fusions to plot
countID	column name to count recurrent fusions SampleID/ParticipantID/tumorID
palette_rec	colors for grouping variables
base_size	Numeric, size of font for plot

Value

A ggplot object containing an overview on the recurrent fused genes

Examples

out_annofuse <- system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
sfc <- read.delim(out_annofuse, stringsAsFactors = FALSE)
# keep only in-frame and fusions where both breakpoints are within genes
sfc <- as.data.frame(
  sfc[which(sfc$Fusion_Type == "in-frame" & sfc$BreakpointLocation == "Genic"), ]
)
plot_recurrent_genes(sfc, groupby = "broad_histology", countID = "Kids_First_Participant_ID")

d3b-center/annoFuse documentation built on Oct. 2, 2024, 4:17 a.m.