plot_granges() creates a Shiny app that displays a
Gosling plot of a given GRanges object. It visualizes genomic
ranges with both rectangle and point representations, and
allows for customization of the plot title and subtitle.
Usage
gosling_plot(
granges,
title = "GRanges Plot",
subtitle = "Stacked nucleotide example",
plot_type = c("bar", "lollipop"),
create_app = interactive()
)Arguments
- granges
A
GenomicRanges::GRanges(e.g.,GenomicRanges::GPos) object containing the genomic ranges to be plotted.- title
character(1) Title of the plot. Default is "GRanges Plot".
- subtitle
character(1) The subtitle of the plot. Default is "Stacked nucleotide example".
- plot_type
character(1) Select the type of gosling plot. Default is "bar"; available types are described in Details.
- create_app
logical(1) Produce a Shiny app for Gosling visualization. Default
TRUEwhen used interactively.
Value
gosling_plot() with create_app = TRUE returns a
shinyApp object that, when run, displays the Gosling
plot. When create_app = FALSE, the (invisible) return value
represents the gosling object to be used in Shiny apps.
Details
The function supports 2 types of plots as selected through the
plot_type argument: (1) "bar": a barplot-like view of the
pathogenicity score at each position, similar to a sequencing
coverage plot, and (2) "lollipop": a lollipop plot focusing on
the pathogenicity classification (ambiguous, benign, pathogenic) at
each position. It requires that the GenomicRanges::GRanges
object has the following metadata columns: 'am_class' (effect
classification),'am_pathogenicity' (pathogenicity score), 'ALT'
(alternative allele) and 'REF' (reference allele).
Examples
## Create a sample GRanges object from AlphamissenseR
gpos <-
am_data("hg38") |>
filter(uniprot_id == "Q1W6H9") |>
to_GPos()
## Plot `gpos` using shiny.gosling
if (requireNamespace("shiny.gosling", quietly = TRUE)) {
gosling_plot(
gpos, title = "Q1W6H_track", subtitle = "bar plot example",
plot_type = "bar", create_app = FALSE
)
}