plot_fusion {chimeraviz} | R Documentation |
This function creates a plot with information about transcripts, coverage, location and more.
plot_fusion( fusion, edb = NULL, bamfile = NULL, which_transcripts = "exonBoundary", ylim = c(0, 1000), non_ucsc = TRUE, reduce_transcripts = FALSE, bedgraphfile = NULL ) plot_fusion_separate( fusion, edb, bamfile = NULL, which_transcripts = "exonBoundary", ylim = c(0, 1000), non_ucsc = TRUE, reduce_transcripts = FALSE, bedgraphfile = NULL ) plot_fusion_together( fusion, edb, bamfile = NULL, which_transcripts = "exonBoundary", ylim = c(0, 1000), non_ucsc = TRUE, reduce_transcripts = FALSE, bedgraphfile = NULL )
fusion |
The Fusion object to plot. |
edb |
The ensembldb object that will be used to fetch data. |
bamfile |
The bamfile with RNA-seq data. |
which_transcripts |
This character vector decides which transcripts are to be plotted. Can be "exonBoundary", "withinExon", "withinIntron", "intergenic", or a character vector with specific transcript ids. Default value is "exonBoundary". |
ylim |
Limits for the coverage y-axis. |
non_ucsc |
Boolean indicating whether or not the bamfile used has UCSC- styled chromosome names (i.e. with the "chr" prefix). Setting this to true lets you use a bamfile with chromosome names like "1" and "X", instead of "chr1" and "chrX". |
reduce_transcripts |
Boolean indicating whether or not to reduce all transcripts into a single transcript for each partner gene. |
bedgraphfile |
A bedGraph file to use instead of the bamfile to plot coverage. |
plot_fusion() will dispatch to either plot_fusion_separate() or plot_fusion_together(). plot_fusion_separate() will plot the fusion gene partners in separate graphs shown next to each other, while plot_fusion_together() will plot the fusion gene partners in the same graph with the same x-axis. plot_fusion() will dispatch to plot_fusion_together() if the fusion gene partners are on the same strand, same chromosome and are close together (<=50,000 bp apart).
Creates a fusion plot.
# 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) # 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") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 1000, height = 750) # Plot! plot_fusion( fusion = fusion, bamfile = bamfile5267, edb = edb, non_ucsc = TRUE) # Close device dev.off() # Example using a .bedGraph file instead of a .bam file: # 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) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bedgraphfile with coverage data from the regions of this fusion event bedgraphfile <- system.file( "extdata", "fusion5267and11759reads.bedGraph", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 1000, height = 750) # Plot! plot_fusion( fusion = fusion, bedgraphfile = bedgraphfile, edb = edb, non_ucsc = TRUE) # Close device dev.off()