plot_sashimi: Visualise RNA-seq data in a the form of a sashimi plot

In dasper: Detecting abberant splicing events from RNA-sequencing data

Description

plot_sashimi plots the splicing events and coverage over a specific genes/transcript and/or genomic region of interest. The plotting are built from ggplot2 functions.

Usage

plot_sashimi(
  junctions,
  ref,
  gene_tx_id,
  case_id = NULL,
  sum_func = mean,
  region = NULL,
  annot_colour = c(ggpubr::get_palette("jco", 1), ggpubr::get_palette("npg", 7)[c(1, 3,
    2, 5, 6)], ggpubr::get_palette("jco", 6)[c(3)]),
  digits = 2,
  count_label = TRUE
)

Arguments

junctions	junction data as a RangedSummarizedExperiment-class object.
ref	either path to gtf/gff3 or object of class TxDb-class.
gene_tx_id	gene name as ensembl id, ensembl transcript id or gene name.
case_id	list of one element. This must be a character vector containing the
sum_func	list of one element. This must be a character vector containing the
region	a GenomicRanges of length 1 that is used to filter the exons/junctions. Only those that overlap this region are plotted.
annot_colour	character vector of colours for junction types. One value must be supplied labelling each of the 7 possible types.
digits	used in round, specifying the number of digits to round the junction counts to for visualisation purposes.
count_label	logical value specifying whether to add label the count of each junction.

Value

ggplot displaying the splicing (and coverage) surrounding the transcript/region of interest.

Examples

# use GenomicState to load txdb (GENCODE v31)
ref <- GenomicState::GenomicStateHub(
    version = "31",
    genome = "hg38",
    filetype = "TxDb"
)[[1]]

junctions_processed <- junction_process(
    junctions_example,
    ref,
    types = c("ambig_gene", "unannotated")
)

sashimi_plot <- plot_sashimi(
    junctions = junction_filter(junctions_processed),
    ref = ref,
    gene_tx_id = "ENSG00000142156.14",
    sum_func = NULL
)

dasper documentation built on Nov. 8, 2020, 7:28 p.m.