plot_recurrent_genes: Function to plot recurrent fused genes

Description Usage Arguments Value Examples

View source: R/plot_recurrent_genes.R

Description

Function to plot recurrent fused genes

Usage

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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

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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 March 11, 2021, 9:05 p.m.