browser_ui = function(id, all_exp, browser_options, gene_names_init,
libs, label = "Browser") {
ns <- NS(id)
genomes <- unique(all_exp$organism)
experiments <- all_exp$name
init_tx <- gene_names_init[label == browser_options["default_gene"],]
init_libs <- unlist(strsplit(browser_options["default_libs"], "\\|"))
copy_button_formatting <- tags$head(
tags$style(HTML('#clip{background-color:orange}'))
)
tabPanel(
tags$head(includeHTML(system.file("google_analytics_html",
"google_analytics.html", package = "RiboCrypt"))),
title = "browser", icon = icon("chart-line"),
sidebarLayout(
jqui_resizable(sidebarPanel(
tabsetPanel(
tabPanel("Browser",
organism_input_select(c("ALL", genomes), ns),
experiment_input_select(experiments, ns, browser_options),
gene_input_select(ns, FALSE, browser_options),
tx_input_select(ns, FALSE, init_tx),
library_input_select(ns, TRUE, libs, init_libs),
frame_type_select(ns, selected =
browser_options["default_frame_type"]),
sliderInput(ns("kmer"), "K-mer length", min = 1, max = 20,
value = as.numeric(browser_options["default_kmer"])),
helper_button_redirect_call(), # Here are settings ->
shinyjs::useShinyjs(),
rclipboardSetup(),
copy_button_formatting
),
tabPanel("Settings",
numericInput(ns("extendLeaders"), "5' extension", 0),
numericInput(ns("extendTrailers"), "3' extension", 0),
textInput(ns("customSequence"), label = "Custom sequences highlight", value = NULL),
textInput(ns("genomic_region"), label = "Genomic region", value = NULL),
checkboxInput(ns("viewMode"), label = "Genomic View", value = FALSE),
checkboxInput(ns("useCustomRegions"), label = "Protein structures", value = FALSE),
checkboxInput(ns("other_tx"), label = "Full annotation", value = FALSE),
checkboxInput(ns("add_uorfs"), label = "uORF annotation", value = FALSE),
checkboxInput(ns("add_translon"), label = "Predicted translons", value = FALSE),
checkboxInput(ns("log_scale"), label = "Log Scale", value = FALSE),
checkboxInput(ns("expression_plot"), label = "Add expression plot", value = FALSE),
checkboxInput(ns("phyloP"), label = "phyloP", value = FALSE),
checkboxInput(ns("withFrames"), label = "Split color Frames", value = TRUE),
checkboxInput(ns("summary_track"), label = "Summary top track", value = FALSE),
frame_type_select(ns, "summary_track_type", "Select summary display type"),
uiOutput(ns("clip")),
export_format_of_plot(ns)
)
),
actionButton(ns("go"), "Plot", icon = icon("rocket")), width=3
)),
mainPanel(
jqui_resizable(plotlyOutput(outputId = ns("c"), height = "500px")) %>% shinycssloaders::withSpinner(color="#0dc5c1"),
plotlyOutput(outputId = ns("e"), height = "50px"),
uiOutput(ns("variableUi"),),
plotlyOutput(outputId = ns("d")) %>% shinycssloaders::withSpinner(color="#0dc5c1"), width=9)
)
)
}
browser_server <- function(id, all_experiments, env, df, experiments,
tx, cds, libs, org, gene_name_list, rv,
browser_options) {
moduleServer(
id,
function(input, output, session, all_exp = all_experiments) {
study_and_gene_observers(input, output, session)
output$clip <- renderUI({clipboard_url_button(input, session)})
# Main plot controller, this code is only run if 'plot' is pressed
mainPlotControls <- eventReactive(input$go,
click_plot_browser_main_controller(input, tx, cds, libs, df),
ignoreInit = check_plot_on_start(browser_options),
ignoreNULL = FALSE)
bottom_panel <- reactive(bottom_panel_shiny(mainPlotControls)) %>%
bindCache(mainPlotControls()$hash_bottom) %>%
bindEvent(mainPlotControls(), ignoreInit = FALSE, ignoreNULL = TRUE)
output$c <- renderPlotly(browser_track_panel_shiny(mainPlotControls, bottom_panel(), session)) %>%
bindCache(mainPlotControls()$hash_browser) %>%
bindEvent(bottom_panel(), ignoreInit = FALSE, ignoreNULL = TRUE)
# Protein display
module_protein(input, output, gene_name_list, session)
output$d <- renderPlotly({
req(input$expression_plot == TRUE)
click_plot_boxplot(mainPlotControls, session)}) %>%
bindCache(mainPlotControls()$hash_expression)
return(rv)
}
)
}
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