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formatting changes so pull request follows package style
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- run devtools::document() (renames man page to plot_granges.Rd, etc.)
- standardize roxygen documentation formatting
- update example argument 'mode = ' to 'plot_type = '
- use match.args() for plot_type argument validation
- avoid long lines and extra vertical spacing
- use standard code indentation in vignette
- do not use inline links []()
- wrap vignette text to 80 columns
- remove trailing whitespace
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@mtmorgan
mtmorgan committed Sep 24, 2024
1 parent 448cc7e commit 79d6751
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251 changes: 135 additions & 116 deletions R/plot_granges.R
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Original file line number Diff line number Diff line change
@@ -1,39 +1,41 @@
#' @rdname plot_granges
#'
#' @title Plot a GRanges object using Shiny and Gosling
#' @title Plot a GRanges Object Using Shiny and Gosling
#'
#' @description This function creates a Shiny app that displays a
#' @description `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.

#'
#' @details
#' The function supports 2 types of plots as selected through the `plot_type`
#' argument: (1) a barplot-like view of the pathogenicity score at each position,
#' similar to a sequencing coverage plot, and (2) a lollipop plot focusing on
#' the pathogenicity classification (ambiguous, benign, pathogenic) at each
#' position. It requires that the [`GRanges`] object has the following metadata
#' columns: 'am_class' (effect classification),'am_pathogenicity'
#' (pathogenicity score), 'ALT' (alternative allele) and 'REF'
#' (reference allele).

#' @param gr A [`GRanges`] object containing the genomic ranges to
#' be plotted.
#'
#' The function supports 2 types of plots as selected through the
#' `plot_type` argument: (1) `"bars"`: 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 [`GRanges`] object has the
#' following metadata columns: 'am_class' (effect
#' classification),'am_pathogenicity' (pathogenicity score), 'ALT'
#' (alternative allele) and 'REF' (reference allele).
#'
#' @param gr A [`GRanges`] object containing the genomic ranges to be
#' plotted.
#'
#' @param title character(1) Title of the plot. Default is
#' "GRanges Plot".
#' @param subtitle character(1) The subtitle of the plot. Default
#' is "Stacked nucleotide example".
#' @param plot_type character(1) Select the type of gosling plot.
#' Default is "bars".
#' - "bars": Stacked bar plot with height based on pathogenicity score,
#' - "lollipop": variation of a bar chart where the bar is replaced with a
#' line and a dot at the end to show mutation variations.
#'
#' @param subtitle character(1) The subtitle of the plot. Default is
#' "Stacked nucleotide example".
#'
#' @param plot_type character(1) Select the type of gosling plot.
#' Default is "bars"; available types are described in Details.
#'
#' @return A `shinyApp` object that, when run, displays the Gosling
#' plot.
#'
#' @note This function requires the `shiny`, `shiny.gosling`, and `GenomicRanges`
#' packages to be installed.
#' @note This function requires the `shiny`, `shiny.gosling`, and
#' `GenomicRanges` packages to be installed.
#'
#' @examples
#' if (requireNamespace("GenomicRanges")) {
Expand All @@ -45,39 +47,40 @@
#' to_GPos()
#'
#' ## Plot the GRanges object
#' plot_granges(
#' gpos, mode = "bar", title = "Q1W6H_track",
#' subtitle = "bar plot example"
#' )
#'}
#'
#' plot_granges(
#' gpos, title = "Q1W6H_track", subtitle = "bar plot example",
#' plot_type = "bars"
#' )
#'
#' }
#'
#' @export
plot_granges <-
function(gr_input,
title = "GRanges Plot",
subtitle = "Stacked nucleotide example",
plot_type = "bars")
function(
gr_input,
title = "GRanges Plot",
subtitle = "Stacked nucleotide example",
plot_type = c("bars", "lollipop")
)
{
## Validate input
stopifnot(
is(granges, "GRanges"),
isScalarCharacter(title),
isScalarCharacter(subtitle),
isScalarCharacter(plot_type)
)
is(gr_input, "GRanges"),
isScalarCharacter(title),
isScalarCharacter(subtitle)
)
plot_type <- match.arg(plot_type)

## Define categories and color mapping
categories <- c("likely_benign", "ambiguous", "likely_pathogenic")
colormapping <- c("#89d5f5", "gray", "#f56c6c")

## Turns out gr must be coerced to GRanges(), will look into this later
gr_input <- as(gr_input, "GRanges")
## Get range from GRanges object
r <- range(gr_input)
# This fixes the bug if .gosling directory does not already exist

## This fixes the bug if .gosling directory does not already exist
if (!dir.exists(".gosling")){
dir.create(".gosling")
}
Expand All @@ -89,10 +92,9 @@ plot_granges <-
genomicFields = c("start", "end")
)


## trigger the option for bars or lollipop
if (identical(plot_type, "bars")){
#define single track
## trigger the option for bars or lollipop
if (identical(plot_type, "bars")) {
## define single track
track_bar <- shiny.gosling::add_single_track(
width = 800,
height = 180,
Expand All @@ -101,19 +103,25 @@ plot_granges <-
x = shiny.gosling::visual_channel_x(
field = "start", type = "genomic", axis = "bottom"
),
xe = shiny.gosling::visual_channel_x(field = "end", type = "genomic"),
xe = shiny.gosling::visual_channel_x(
field = "end", type = "genomic"
),
y = shiny.gosling::visual_channel_y(
field = "am_pathogenicity", type = "quantitative", axis = "right"
field = "am_pathogenicity", type = "quantitative",
axis = "right"
),
color = shiny.gosling::visual_channel_color(
field = "am_pathogenicity",
type = "quantitative"
),
tooltip = shiny.gosling::visual_channel_tooltips(
shiny.gosling::visual_channel_tooltip(field = "REF", type = "nominal",
alt = "Reference"),
shiny.gosling::visual_channel_tooltip(field = "ALT", type = "nominal",
alt = "Alternative / Mutation"),
shiny.gosling::visual_channel_tooltip(
field = "REF", type = "nominal", alt = "Reference"
),
shiny.gosling::visual_channel_tooltip(
field = "ALT", type = "nominal",
alt = "Alternative / Mutation"
),
shiny.gosling::visual_channel_tooltip(
field = "am_pathogenicity",
type = "quantitative",
Expand All @@ -122,79 +130,90 @@ plot_granges <-
) ),
size = list(value = 5)
)

composed_view <- shiny.gosling::compose_view(
layout = "linear",
xDomain = list(chromosome = as.character(seqnames(r)),
interval = c(start(r), end(r))),
xDomain = list(
chromosome = as.character(seqnames(r)),
interval = c(start(r), end(r))
),
tracks = track_bar

)
## other option

## other option
} else if (identical(plot_type, "lollipop")){

## Define multi tracks
track_ref <- shiny.gosling::add_single_track(
data = track_data,
mark = "rect",
x = shiny.gosling::visual_channel_x(field = "start", type = "genomic", axis = "top"),
xe = shiny.gosling::visual_channel_x(field = "end", type = "genomic"),
size = list(value = 50),
stroke = "lightgrey",
strokeWidth = list(value = 1),
opacity = list(value = 0.3)
)
## Define multi tracks
track_ref <- shiny.gosling::add_single_track(
data = track_data,
mark = "rect",
x = shiny.gosling::visual_channel_x(
field = "start", type = "genomic", axis = "top"
),
xe = shiny.gosling::visual_channel_x(
field = "end", type = "genomic"
),
size = list(value = 50),
stroke = "lightgrey",
strokeWidth = list(value = 1),
opacity = list(value = 0.3)
)

track_alt <- shiny.gosling::add_single_track(
data = track_data,
mark = "point",
x = shiny.gosling::visual_channel_x(field = "start", type = "genomic", axis = "top"),
xe = shiny.gosling::visual_channel_x(field = "end", type = "genomic"),
y = shiny.gosling::visual_channel_y(field = "am_class", type="nominal",
domain= categories, axis = "left",baseline = "ambiguous" ),
text = list(field = "ALT", type = "nominal"),
size = list(value = 5),
tooltip = shiny.gosling::visual_channel_tooltips(
shiny.gosling::visual_channel_tooltip(field = "REF", type = "nominal",
alt = "Reference"),
shiny.gosling::visual_channel_tooltip(field = "ALT", type = "nominal",
alt = "Alternative / Mutation"),
shiny.gosling::visual_channel_tooltip(
field = "am_pathogenicity",
type = "quantitative",
alt = "AM_Pathogenicity Score",
format = "0.2"
) )
)
track_alt <- shiny.gosling::add_single_track(
data = track_data,
mark = "point",
x = shiny.gosling::visual_channel_x(
field = "start", type = "genomic", axis = "top"
),
xe = shiny.gosling::visual_channel_x(
field = "end", type = "genomic"
),
y = shiny.gosling::visual_channel_y(
field = "am_class", type="nominal", domain= categories,
axis = "left",baseline = "ambiguous"
),
text = list(field = "ALT", type = "nominal"),
size = list(value = 5),
tooltip = shiny.gosling::visual_channel_tooltips(
shiny.gosling::visual_channel_tooltip(
field = "REF", type = "nominal", alt = "Reference"
),
shiny.gosling::visual_channel_tooltip(
field = "ALT", type = "nominal",
alt = "Alternative / Mutation"
),
shiny.gosling::visual_channel_tooltip(
field = "am_pathogenicity",
type = "quantitative",
alt = "AM_Pathogenicity Score",
format = "0.2"
)
)
)

## Compose view
composed_view <- shiny.gosling::compose_view(
width = 800,
height = 180,
multi = TRUE,
layout = "linear",
xDomain = list(
chromosome = as.character(seqnames(r)),
interval = c(start(r), end(r))
),
alignment = "overlay",
color = shiny.gosling::visual_channel_color(
field = "am_class",
type = "nominal",
domain = categories,
baseline = "ambiguous",
range = colormapping,
legend = TRUE
),
tracks = shiny.gosling::add_multi_tracks(track_ref, track_alt)
)

}
## trigger check
else {
stop("Invalid plot_type. Use 'bars' or 'lollipop'")
## Compose view
composed_view <- shiny.gosling::compose_view(
width = 800,
height = 180,
multi = TRUE,
layout = "linear",
xDomain = list(
chromosome = as.character(seqnames(r)),
interval = c(start(r), end(r))
),
alignment = "overlay",
color = shiny.gosling::visual_channel_color(
field = "am_class",
type = "nominal",
domain = categories,
baseline = "ambiguous",
range = colormapping,
legend = TRUE
),
tracks = shiny.gosling::add_multi_tracks(track_ref, track_alt)
)
}

## Arrange into view
arranged_view3 <- shiny.gosling::arrange_views(
title = title,
Expand Down
69 changes: 69 additions & 0 deletions man/plot_granges.Rd
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