plot_fusion_transcript_with_protein_domain {chimeraviz} | R Documentation |
This function takes a fusion object, an ensembldb object, a bedfile with protein domain data and two specific transcript ids. The function plots the specific fusion transcript along with annotations of protein domains. If a bamfile is specified, the fusion transcript will be plotted with coverage information.
plot_fusion_transcript_with_protein_domain( fusion, edb = NULL, bamfile = NULL, bedfile = NULL, gene_upstream_transcript = "", gene_downstream_transcript = "", plot_downstream_protein_domains_if_fusion_is_out_of_frame = FALSE )
fusion |
The Fusion object to plot. |
edb |
The edb object that will be used to fetch data. |
bamfile |
The bamfile with RNA-seq data. |
bedfile |
The bedfile with protein domain data. |
gene_upstream_transcript |
The transcript id for the upstream gene. |
gene_downstream_transcript |
The transcript id for the downstream gene. |
plot_downstream_protein_domains_if_fusion_is_out_of_frame |
Setting this to true makes the function plot protein domains in the downstream gene even though the fusion is out of frame. |
Note that the transcript database used (the edb object) must have the same seqnames as any bamfile used. Otherwise the coverage data will be wrong.
Creates a fusion transcript plot with annotations of protein domains.
# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Select transcripts gene_upstream_transcript <- "ENST00000434290" gene_downstream_transcript <- "ENST00000370031" # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bamfile with reads in the regions of this fusion event bamfile5267 <- system.file( "extdata", "fusion5267and11759reads.bam", package="chimeraviz") # bedfile with protein domains for the transcripts in this example bedfile <- system.file( "extdata", "protein_domains_5267.bed", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_fusion_transcript_with_protein_domain( fusion = fusion, edb = edb, bamfile = bamfile5267, bedfile = bedfile, gene_upstream_transcript = gene_upstream_transcript, gene_downstream_transcript = gene_downstream_transcript, plot_downstream_protein_domains_if_fusion_is_out_of_frame = TRUE) # Close device dev.off()