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

Description Usage Arguments Value

View source: R/sashimi_plot.R

Description

plot_sashimi plots the splicing events and coverage over a specific transcript and/or genomic region of interest. Centres around ggplot functions.

Usage

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plot_sashimi(gene_tx_to_plot, region_to_plot = NULL, junc_metadata,
  junc_counts_case, junc_counts_ctrl = NULL, coverage_case = NULL,
  coverage_ctrl = NULL, ref, add_junc_label = F, binwidth = 50)

Arguments

gene_tx_to_plot

gr. Currently only accepts an ensembl transcript id that is found in the ref input. In future, this may be extended to plot genes, however need to think about how to plot the gene_track

region_to_plot

gr. Only plot exons and juncs that overlap this region and are connected to gene_tx_to_plot

junc_metadata

gr. Junction details. Essentially must contain the co-ordinates of the junctions to plot and annotation of junctions by acceptor/donor using annotate_junc_ref

junc_counts_case

num. Vector containing the counts of cases with same order and length as junc_metadata

junc_counts_ctrl

num. Vector containing the counts of ctrls same order and length as junc_metadata

coverage_case

chr. Path to the bw object of case. Leave as NULL if you don't want this to be plotted.

ref

gr. gtf annotation imported through rtracklayer.

Value

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


dzhang32/RNAdiagnosR documentation built on Dec. 5, 2019, 2 a.m.