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refactor plot_granges() as gosling_plot()
- rename as gosling_plot(); renames files to Gosling.R / Gosling.Rd
- test for required packages as part of argument validation ('fail early')
- rename 'bars' option as 'bar', for consistency with gosling terminology
- separate compose_view_bar() and compose_view_lollipop() for code
modularity
- separate gosling_app() for Shiny app creation. Only create app when
create_app = TRUE (default when interactive()); facilitates running
code in examples / vignettes during R CMD check
- revise example to maximize code run during R CMD check
- rename argument as `granges`, so users are less likely to puzzle over
`gr_` meaning
- managing location of .gosling so that it is not created in the user
working directory. Uses setwd() / on.exit() because shiny.gosling does
not allow easy alternative specification
- link [`GenomicRanges::GRanges`] in man page to satisfy R CMD check
- version bump and NEWS update- Loading branch information
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,269 @@ | ||
| gosling_view_bar <- | ||
| function(rng, track_data) | ||
| { | ||
| ## define single track | ||
| track_bar <- shiny.gosling::add_single_track( | ||
| width = 800, | ||
| height = 180, | ||
| data = track_data, | ||
| mark = "bar", | ||
| x = shiny.gosling::visual_channel_x( | ||
| field = "start", type = "genomic", axis = "bottom" | ||
| ), | ||
| xe = shiny.gosling::visual_channel_x(field = "end", type = "genomic"), | ||
| y = shiny.gosling::visual_channel_y( | ||
| 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 = "am_pathogenicity", type = "quantitative", | ||
| alt = "AM_Pathogenicity Score", format = "0.2" | ||
| ) | ||
| ), | ||
| size = list(value = 5) | ||
| ) | ||
|
|
||
| shiny.gosling::compose_view( | ||
| layout = "linear", | ||
| xDomain = list( | ||
| chromosome = as.character(GenomicRanges::seqnames(rng)), | ||
| interval = c(GenomicRanges::start(rng), GenomicRanges::end(rng)) | ||
| ), | ||
| tracks = track_bar | ||
| ) | ||
| } | ||
|
|
||
| gosling_view_lollipop <- | ||
| function(rng, track_data) | ||
| { | ||
| ## Define categories and color mapping | ||
| categories <- c("likely_benign", "ambiguous", "likely_pathogenic") | ||
| colormapping <- c("#89d5f5", "gray", "#f56c6c") | ||
|
|
||
| ## 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" | ||
| ) | ||
| ) | ||
| ) | ||
|
|
||
| ## Compose view | ||
| shiny.gosling::compose_view( | ||
| width = 800, | ||
| height = 180, | ||
| multi = TRUE, | ||
| layout = "linear", | ||
| xDomain = list( | ||
| chromosome = as.character(GenomicRanges::seqnames(rng)), | ||
| interval = c(GenomicRanges::start(rng), GenomicRanges::end(rng)) | ||
| ), | ||
| 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) | ||
| ) | ||
| } | ||
|
|
||
| gosling_app <- | ||
| function(view) | ||
| { | ||
| ## Create Shiny app | ||
| ui <- shiny::fluidPage( | ||
| shiny.gosling::use_gosling(clear_files = FALSE), | ||
| shiny.gosling::goslingOutput("gosling_plot") | ||
| ) | ||
|
|
||
| server <- function(input, output, session) { | ||
| output$gosling_plot <- shiny.gosling::renderGosling({ | ||
| shiny.gosling::gosling(component_id = "component_3", view) | ||
| }) | ||
| } | ||
|
|
||
| ## Return the Shiny app | ||
| shiny::shinyApp(ui, server) | ||
| } | ||
|
|
||
| #' @rdname Gosling | ||
| #' | ||
| #' @title Plot a GPos or GRanges Object Using Shiny and Gosling | ||
| #' | ||
| #' @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) `"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). | ||
| #' | ||
| #' @param granges A [`GenomicRanges::GRanges`] (e.g., | ||
| #' [`GenomicRanges::GPos`]) 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 "bar"; available types are described in Details. | ||
| #' | ||
| #' @param create_app logical(1) Produce a Shiny app for Gosling | ||
| #' visualization. Default `TRUE` when used interactively. | ||
| #' | ||
| #' @return `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. | ||
| #' | ||
| #' @note This function requires the `shiny`, `shiny.gosling`, and | ||
| #' `GenomicRanges` packages to be installed. | ||
| #' | ||
| #' @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 | ||
| #' ) | ||
| #' } | ||
| #' | ||
| #' @importFrom tools R_user_dir | ||
| #' | ||
| #' @importFrom methods as | ||
| #' | ||
| #' @export | ||
| gosling_plot <- | ||
| function( | ||
| granges, | ||
| title = "GRanges Plot", | ||
| subtitle = "Stacked nucleotide example", | ||
| plot_type = c("bar", "lollipop"), | ||
| create_app = interactive() | ||
| ) | ||
| { | ||
| ## Validate input | ||
| stopifnot( | ||
| is(granges, "GRanges"), | ||
| isScalarCharacter(title), | ||
| isScalarCharacter(subtitle), | ||
| isScalarLogical(create_app), | ||
| requireNamespace("GenomicRanges", quietly = TRUE), | ||
| requireNamespace("shiny.gosling", quietly = TRUE) | ||
| ) | ||
| plot_type <- match.arg(plot_type) | ||
|
|
||
| ## Turns out gr must be coerced to GRanges(), will look into this later | ||
| granges <- as(granges, "GRanges") | ||
| ## Get range from GRanges object | ||
| rng <- range(granges) | ||
|
|
||
| ## avoid writing '.gosling' to current working directory; awkward | ||
| ## because shiny.gosling uses the working directory. | ||
| cache <- R_user_dir("AlphaMissenseR", which = "cache") | ||
| gosling_cache <- file.path(cache, ".gosling") | ||
| if (!dir.exists(gosling_cache)) { | ||
| status <- dir.create(gosling_cache, recursive = TRUE) | ||
| if (!status) | ||
| stop("failed to create gosling cache '", gosling_cache, "'") | ||
| } | ||
| original_wd <- getwd() | ||
| on.exit(setwd(original_wd)) | ||
| setwd(cache) # so that '.gosling' is available to shiny.gosling | ||
|
|
||
| ## Prepare track data | ||
| track_data <- shiny.gosling::track_data_gr( | ||
| granges, | ||
| chromosomeField = "seqnames", | ||
| genomicFields = c("start", "end") | ||
| ) | ||
|
|
||
| composed_view <- switch( | ||
| plot_type, | ||
| bar = gosling_view_bar(rng, track_data), | ||
| lollipop = gosling_view_lollipop(rng, track_data), | ||
| stop("unknown `plot_type = '", plot_type, "'`") | ||
| ) | ||
|
|
||
| ## Arrange into view | ||
| arranged_view <- shiny.gosling::arrange_views( | ||
| title = title, | ||
| subtitle = subtitle, | ||
| views = composed_view | ||
| ) | ||
|
|
||
| if (create_app) { | ||
| gosling_app(arranged_view) | ||
| } else { | ||
| ## return arranged_view invisibly | ||
| invisible(arranged_view) | ||
| } | ||
| } |
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