Nothing
ui.modules_1_tcga_01 = function(id){
ns = NS(id)
main_ui = tagList(
mol_quick_select_UI(ns("id"), "tcga", c("mRNA","transcript","methylation","miRNA")),
h4("3. Select analysis mode"),
shinyWidgets::prettyRadioButtons(
inputId = ns("Mode"), label = NULL,
choiceValues = c("Pan-cancer", "Single-cancer"),
choiceNames = c("Pan-cancer", "Single-cancer"),
animation = "jelly"
),
tabsetPanel(
id = ns("Mode_params"),
type = "hidden",
tabPanel("Single-cancer",
selectInput(ns("Cancer"), "Select one cancer",sort(tcga_names))
),
tabPanel("Pan-cancer")
),
h4("4. Include GTEx normal samples"),
switchInput(
inputId = ns("pdist_dataset"),
value = TRUE,
onLabel = "Yes",
offLabel = "No"
),
shinyWidgets::actionBttn(
inputId = ns("search_bttn"),
label = "Go!",
style = "gradient",
icon = icon("search"),
color = "primary",
block = TRUE,
size = "sm"
)
)
out_ui = tagList(
fluidRow(
uiOutput(ns("gene_pancan_dist")),
)
)
side_ui = tagList(
fluidRow(
column(6,
h4("1. Visualization parameters"),
h5("(1) Geometry type:"),
awesomeRadio(ns("pdist_mode"), label = NULL,
choices = c("Boxplot", "Violinplot"), selected = "Boxplot", inline = TRUE),
h5("(2) Label type:"),
awesomeRadio(ns("pdist_show_p"), label = NULL,
choices = c("None", "P value", "P label"), selected = "None", inline = TRUE),
h5("(3) Colors:"),
colourpicker::colourInput(inputId = ns("tumor_col"), "Tumor sample color", "#DF2020"),
colourpicker::colourInput(inputId = ns("normal_col"), "Normal sample color", "#DDDF21"),
h5("(4) ggplot theme:"),
selectInput(inputId = ns("theme"), label = "Select theme for plot",
choices = names(themes_list), selected = "Cowplot"),
),
column(6,
h4("2. Download options"),
h5("(1) Figure:"),
numericInput(inputId = ns("height"), label = "Height", value = 5),
numericInput(inputId = ns("width"), label = "Width", value = 12),
awesomeRadio(ns("device"), label = "Format",
choices = c("pdf", "png"), selected = "pdf", inline = TRUE),
downloadBttn(
outputId = ns("download_1"),
style = "gradient",
color = "primary",
block = TRUE,
size = "sm"
),
h5("(2) Data table:"),
downloadBttn(
outputId = ns("download_2"),
style = "gradient",
color = "primary",
block = TRUE,
size = "sm"
)
)
)
)
fluidPage(
style = "height:600px",
box(main_ui,
width = 5,
solidHeader = TRUE,
title = "Quick TCGA Analysis: Compare between tumor and normal",
status = "primary",
background = "gray",
collapsible = FALSE,
style = "height:600px",
footer = "TIPs: Click the bottom button to execute/update the analysis."
),
box(out_ui,
width = 7,
solidHeader = TRUE,
title = "Analytical results:",
status = "primary",
background = "gray",
collapsible = FALSE,
style = "height:600px",
footer = "TIPs: Pull the sidebar to adjsut plot parameters or download results through the top-right widget.",
sidebar = boxSidebar(
id = ns("sidebar"),
width = 50,
side_ui
)
)
)
}
server.modules_1_tcga_01 = function(input, output, session){
ns = session$ns
observeEvent(input$Mode, {
updateTabsetPanel(inputId = "Mode_params", selected = input$Mode)
})
mol_info = callModule(mol_quick_select_Server, "id", "tcga")
mark_p = reactiveValues(Show.P.value=FALSE, Show.P.label=FALSE)
observe({
if(input$pdist_show_p=="P value"){
mark_p$Show.P.value = TRUE
} else if (input$pdist_show_p=="P label") {
mark_p$Show.P.label = TRUE
}
})
observeEvent(input$Mode, {
if(input$Mode=="Pan-cancer"){
updateAwesomeRadio(session, "pdist_mode", label = NULL,
choices = c("Boxplot", "Violinplot"), selected = "Boxplot", inline = TRUE)
} else {
updateAwesomeRadio(session, "pdist_mode", label = NULL,
choices = c("Dotplot", "Violinplot"), selected = "Violinplot", inline = TRUE)
}
})
plot_func <- eventReactive(input$search_bttn, {
print(input$Mode)
p = switch(input$Mode,
`Pan-cancer` = vis_toil_TvsN(
Gene = mol_info$molecule(),
data_type = mol_info$profile(),
Mode = input$pdist_mode,
Show.P.value = mark_p$Show.P.value,
Show.P.label = mark_p$Show.P.label,
TCGA.only = !input$pdist_dataset,
values = c(input$tumor_col, input$normal_col)
) + themes_list[[input$theme]] +
ggplot2::theme(
axis.text.x = element_text(angle = 45, hjust = .5, vjust = .5),
text = element_text(size = 20)),
`Single-cancer` = vis_toil_TvsN_cancer(
Gene = mol_info$molecule(),
data_type = mol_info$profile(),
Cancer = input$Cancer,
Mode = input$pdist_mode,
Show.P.value = mark_p$Show.P.value,
Show.P.label = mark_p$Show.P.label,
TCGA.only = !input$pdist_dataset,
values = c(input$tumor_col, input$normal_col)
) + themes_list[[input$theme]] +
ggplot2::theme(text = element_text(size = 20),
legend.position = "none")
)
return(p)
})
w <- waiter::Waiter$new(id = ns("plot"), html = waiter::spin_hexdots(), color = "black")
observeEvent(input$search_bttn,{
# check whether valid out plot
shinyjs::disable("search_bttn")
chect_plot = is.null(plot_func())
if(chect_plot){
sendSweetAlert(session, title = "Warning", type = "error", text = "Please select a valid molecule.")
req(chect_plot)
}
output$gene_pancan_dist <- renderUI({
w$show()
if(isolate(input$Mode)=="Pan-cancer"){
output$plot = renderPlot(plot_func())
fluidRow(
column(10, offset = 1,
plotOutput(ns("plot"), height = "580px"),
)
)
} else {
output$plot = renderPlot(plot_func())
fluidRow(
column(6, offset = 3,
plotOutput(ns("plot"), height = "580px"),
)
)
}
})
shinyjs::enable("search_bttn")
})
output$download_1 <- downloadHandler(
filename = function() {
paste0(mol_info$molecule(), "_", mol_info$profile(), "_tumorVSnormal.", input$device)
},
content = function(file) {
p <- plot_func()
if (input$device == "pdf") {
pdf(file, width = input$width, height = input$height)
print(p)
dev.off()
} else {
png(file, width = input$width, height = input$height, res = 600, units = "in")
print(p)
dev.off()
}
}
)
output$download_2 <- downloadHandler(
filename = function() {
paste0(mol_info$molecule(), "_", mol_info$profile(), "_tumorVSnormal.csv")
},
content = function(file) {
data = plot_func()$data %>%
dplyr::rename('Cancer'='tissue', 'Dataset'='dataset', 'Sample'='sample',
'Group'='type2', 'Value'="value") %>%
dplyr::select(Cancer,Dataset,Sample,Group,Value) %>%
dplyr::arrange(Cancer, desc(Dataset), Sample, desc(Group))
write.csv(data, file, row.names = FALSE)
}
)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.