View source: R/plot_recurrent_genes.R
plot_recurrent_genes | R Documentation |
Function to plot recurrent fused genes
plot_recurrent_genes( standardFusioncalls, groupby, plotn = 20, countID, palette_rec = NULL, base_size = 20 )
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 |
A ggplot object containing an overview on the recurrent fused genes
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")
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