plotFusion {chimeraviz} | R Documentation |
This function creates a plot with information about transcripts, coverage, location and more.
plotFusion(fusion, edb = NULL, bamfile = NULL, whichTranscripts = "exonBoundary", ylim = c(0, 1000), nonUCSC = TRUE, reduceTranscripts = FALSE, bedgraphfile = NULL) plotFusionSeparate(fusion, edb, bamfile = NULL, whichTranscripts = "exonBoundary", ylim = c(0, 1000), nonUCSC = TRUE, reduceTranscripts = FALSE, bedgraphfile = NULL) plotFusionTogether(fusion, edb, bamfile = NULL, whichTranscripts = "exonBoundary", ylim = c(0, 1000), nonUCSC = TRUE, reduceTranscripts = 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. |
whichTranscripts |
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. |
nonUCSC |
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". |
reduceTranscripts |
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. |
plotFusion() will dispatch to either plotFusionSeparate() or plotFusionTogether(). plotFusionSeparate() will plot the fusion gene partners in separate graphs shown next to each other, while plotFusionTogether() will plot the fusion gene partners in the same graph with the same x-axis. plotFusion() will dispatch to plotFusionTogether() 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 <- importDefuse(defuse833ke, "hg19", 1) fusion <- getFusionById(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! plotFusion( fusion = fusion, bamfile = bamfile5267, edb = edb, nonUCSC = 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 <- importDefuse(defuse833ke, "hg19", 1) fusion <- getFusionById(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! plotFusion( fusion = fusion, bedgraphfile = bedgraphfile, edb = edb, nonUCSC = TRUE) # Close device dev.off()