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reverting importFrom, cache order
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@lee-t
lee-t committed Aug 7, 2024
1 parent 963a9ff commit 008b5d6
Showing 1 changed file with 33 additions and 33 deletions.
66 changes: 33 additions & 33 deletions R/plot_shinygosling.R
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,6 @@
#' = "bar plot example")
#' }
#'
#'@importFrom shiny.gosling add_single_track compose_view visual_channel_x visual_channel_y add_multi_tracks visual_channel_tooltip visual_channel_tooltips visual_channel_color
#'
#'
#' @export
Expand Down Expand Up @@ -85,48 +84,49 @@ plot_granges <-
## Get range from GRanges object
r <- range(gr)

## Prepare track data
track_data <- shiny.gosling::track_data_gr(
gr,
chromosomeField = "seqnames",
genomicFields = c("start", "end")
)

# This fixes the bug if .gosling directory does not already exist
if (!dir.exists(".gosling")){
dir.create(".gosling")
}
## This does not fix the bug, shiny.gosling is hardcoded to search local wd
# This does not fix the bug, shiny.gosling is hardcoded to search local wd
#cache_dir <- file.path(tools::R_user_dir("AlphaMissenseR", which = "cache"), ".gosling")
#if (!dir.exists(cache_dir))
# ## TODO: check return value to ensure directory is created successfully
# dir.create(cache_dir, recursive = TRUE)
# dir.create(cache_dir, recursive = TRUE)

## Prepare track data
track_data <- shiny.gosling::track_data_gr(
gr,
chromosomeField = "seqnames",
genomicFields = c("start", "end")
)


## trigger the option for bars or lollipop
if (plot_type =="bars"){
#define single track
track_bar <- add_single_track(
track_bar <- shiny.gosling::add_single_track(
width = 800,
height = 180,
data = track_data,
mark = "bar",
x = visual_channel_x(
x = shiny.gosling::visual_channel_x(
field = "start", type = "genomic", axis = "bottom"
),
xe = visual_channel_x(field = "end", type = "genomic"),
y = visual_channel_y(
xe = shiny.gosling::visual_channel_x(field = "end", type = "genomic"),
y = shiny.gosling::visual_channel_y(
field = "am_pathogenicity", type = "quantitative", axis = "right"
),
color = visual_channel_color(
color = shiny.gosling::visual_channel_color(
field = "am_pathogenicity",
type = "quantitative"
),
tooltip = visual_channel_tooltips(
visual_channel_tooltip(field = "REF", type = "nominal",
tooltip = shiny.gosling::visual_channel_tooltips(
shiny.gosling::visual_channel_tooltip(field = "REF", type = "nominal",
alt = "Reference"),
visual_channel_tooltip(field = "ALT", type = "nominal",
shiny.gosling::visual_channel_tooltip(field = "ALT", type = "nominal",
alt = "Alternative / Mutation"),
visual_channel_tooltip(
shiny.gosling::visual_channel_tooltip(
field = "am_pathogenicity",
type = "quantitative",
alt = "AM_Pathogenicity Score",
Expand All @@ -135,7 +135,7 @@ plot_granges <-
size = list(value = 5)
)

composed_view <- compose_view(
composed_view <- shiny.gosling::compose_view(
layout = "linear",
xDomain = list(chromosome = as.character(seqnames(r)),
interval = c(start(r), end(r))),
Expand All @@ -147,7 +147,7 @@ plot_granges <-
} else if (plot_type == "lollipop"){

## Define multi tracks
track_ref <- add_single_track(
track_ref <- shiny.gosling::add_single_track(
data = track_data,
mark = "rect",
x = visual_channel_x(field = "start", type = "genomic", axis = "top"),
Expand All @@ -158,21 +158,21 @@ plot_granges <-
opacity = list(value = 0.3)
)

track_alt <- add_single_track(
track_alt <- shiny.gosling::add_single_track(
data = track_data,
mark = "point",
x = visual_channel_x(field = "start", type = "genomic", axis = "top"),
xe = visual_channel_x(field = "end", type = "genomic"),
y = visual_channel_y(field = "am_class", type="nominal",
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 = visual_channel_tooltips(
visual_channel_tooltip(field = "REF", type = "nominal",
tooltip = shiny.gosling::visual_channel_tooltips(
shiny.gosling::visual_channel_tooltip(field = "REF", type = "nominal",
alt = "Reference"),
visual_channel_tooltip(field = "ALT", type = "nominal",
shiny.gosling::visual_channel_tooltip(field = "ALT", type = "nominal",
alt = "Alternative / Mutation"),
visual_channel_tooltip(
shiny.gosling::visual_channel_tooltip(
field = "am_pathogenicity",
type = "quantitative",
alt = "AM_Pathogenicity Score",
Expand All @@ -181,7 +181,7 @@ plot_granges <-
)

## Compose view
composed_view <- compose_view(
composed_view <- shiny.gosling::compose_view(
width = 800,
height = 180,
multi = TRUE,
Expand All @@ -191,15 +191,15 @@ plot_granges <-
interval = c(start(r), end(r))
),
alignment = "overlay",
color = visual_channel_color(
color = shiny.gosling::visual_channel_color(
field = "am_class",
type = "nominal",
domain = categories,
baseline = "ambiguous",
range = colormapping,
legend = TRUE
),
tracks = add_multi_tracks(track_ref, track_alt)
tracks = shiny.gosling::add_multi_tracks(track_ref, track_alt)
)

}
Expand All @@ -208,7 +208,7 @@ plot_granges <-
stop("Invalid plot_type. Use 'bars' or 'lollipop'")
}
## Arrange into view
arranged_view3 <- arrange_views(
arranged_view3 <- shiny.gosling::arrange_views(
title = title,
subtitle = subtitle,
views = composed_view
Expand Down

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