plot_fusion_transcripts_graph {chimeraviz} | R Documentation |
This function takes a fusion object and a TranscriptDb object and plots a graph showing the possible fusion transcripts.
plot_fusion_transcripts_graph(fusion, edb = NULL, which_transcripts = "exonBoundary", rankdir = "TB")
fusion |
The Fusion object to plot. |
edb |
The edb object that will be used to fetch 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". |
rankdir |
Choose whether the graph should be plotted from left to right ("LR"), or from top to bottom ("TB"). This parameter is given to Rgraphviz::plot(). |
Creates a fusion transcripts graph 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) # 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_transcripts_graph( fusion = fusion, edb = edb) # Close device dev.off()