Description Usage Arguments Value
plot_sashimi
plots the splicing events and coverage over a specific
transcript and/or genomic region of interest. Centres around ggplot
functions.
1 2 3 | 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)
|
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 |
junc_metadata |
gr. Junction details. Essentially must contain the
co-ordinates of the junctions to plot and annotation of junctions by
acceptor/donor using |
junc_counts_case |
num. Vector containing the counts of cases with same
order and length as |
junc_counts_ctrl |
num. Vector containing the counts of ctrls same order
and length as |
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 |
ggplot(s) displaying the splicing and coverage surrounding the transcript/region of interest.
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