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data_rarefying.R
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data_rarefying.R
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linebreaks <- function(n){HTML(strrep(br(), n))}
error_info <- "Invalid operation: Attempt to delete all data"
data_rarefy_ui <- function(id) {
ns <- NS(id)
res <- div(
fluidRow(
column(3,
shinydashboardPlus::box(
width = 12,
title = "Data rarefying",
status = "primary",
collapsible = TRUE,
p("Rarefied species richness for community ecologists."),
p("If the Rare size is 0, default to rarefying according to the minimum sequence count."),
# materialSwitch(ns("rarefying"),
# value = TRUE,
# label = "Data rarefying",
# status = "primary"),
numericInput(ns("raresize"), "Rare Size", 0, 0, 500000, 5000),
br(),
fluidRow(
column(6,
prettyCheckbox(
inputId = ns("trimOTU"),
label = "trim OTU",
value = TRUE,
status = "danger",
shape = "curve"
)
),
column(6,
prettyCheckbox(
inputId = ns("trimSample"),
label = "trim Sample",
value = TRUE,
status = "danger",
shape = "curve"
)
)
),
actionButton(ns("feature"), "Submit")
# br(),
# br(),
# downloadButton(ns("downloadAbu"), "Abundance Table"),
# downloadButton(ns("downloadTax"), "Taxonomy Table")
),
uiOutput(ns("status_summary"))
),
column(9,
uiOutput(ns("overview"))
)
)
)
return(res)
}
data_rarefy_mod <- function(id, mpse) {
moduleServer(
id,
function(input, output, session) {
ns <- session$ns
# res <- eventReactive(input$feature, {
# req(inherits(mpse(), "MPSE"))
# if(input$rarefying){
# res <- mpse() %>% mp_rrarefy
# }else{
# res <- mpse()
# }
# return(res)
# })
mp_rare <- eventReactive(input$feature, {
req(inherits(mpse(), "MPSE"))
raresize <- isolate({
input$raresize
})
if(raresize == 0){
raresize <- NULL
}
mp_rare <- mpse() %>% mp_rrarefy(raresize = raresize,
trimOTU = input$trimOTU,
trimSample = input$trimSample)
return(mp_rare)
})
mp_info <- reactive({
req(inherits(mp_rare(), "MPSE"))
x <- rare_info(mpse(),mp_rare())
return(x)
})
mp_before <- reactive({
req(inherits(mp_rare(), "MPSE"))
x_a <- mpse() %>% mp_extract_assays(.abundance = Abundance) %>% colSums() %>% as.data.frame
#x_r <- mp_rare() %>% mp_extract_assays(.abundance = RareAbundance) %>% colSums() %>% as.data.frame
return(x_a)
})
mp_after <- reactive({
req(inherits(mp_rare(), "MPSE"))
#x_a <- mp_rare() %>% mp_extract_assays(.abundance = Abundance) %>% colSums() %>% as.data.frame
x_r <- mp_rare() %>% mp_extract_assays(.abundance = RareAbundance) %>% colSums() %>% as.data.frame
return(x_r)
})
# mpsum_int <- reactive({
# req(inherits(mpse(), "MPSE"))
# x <- mpse() %>%
# mp_extract_assays(.abundance=Abundance) %>% colSums() %>% as.data.frame
# colnames(x) <- "OTU"
# x$Sample <- rownames(x)
# return(x)
# })
#
#
#
#
# mpsum_btn <- eventReactive(input$feature, {
# req(inherits(mpse(), "MPSE"))
#
# if(input$rarefying){
# abun <- "RareAbundance"
# }else{
# abun <- "Abundance"
# }
# x <- mpse() %>%
# mp_extract_assays(.abundance=!!sym(abun)) %>% colSums() %>% as.data.frame
# colnames(x) <- "OTU"
# x$Sample <- rownames(x)
# return(x)
# })
#
# mpsum <- reactive({
# req(inherits(mpse(), "MPSE"))
# if(input$feature) {
# return(mpsum_btn())
# }else{
# return(mpsum_int())
# }
# })
# #Render overview
output$overview <- renderUI({
req(inherits(mpse(), "MPSE"))
fluidRow(
shinydashboardPlus::box(
width = 12,
title = "Library size (before)",
status = "success",
collapsible = TRUE,
div(
class = "overview_plot",
style = "height:600px; width:95%; overflow:scroll;",
plotOutput(ns("plot_before"), width = "95%", height = paste0(nrow(mp_before()) * 20, "px"))
)
),
shinydashboardPlus::box(
width = 12,
title = "Library size (after)",
status = "success",
collapsible = TRUE,
div(
class = "overview_plot",
style = "height:600px; width:95%; overflow:scroll;",
plotOutput(ns("plot_after"), width = "95%", height = paste0(nrow(mp_after()) * 20, "px"))
)
)
)
})
output$plot_after <- renderPlot(res = 90, {
req(inherits(mp_after(), "data.frame"))
p <- plot_x(mp_after())
return(p)
})
output$plot_before <- renderPlot(res = 90, {
req(inherits(mp_before(), "data.frame"))
p <- plot_x(mp_before())
return(p)
})
output$status_summary <- renderUI({
req(inherits(mp_rare(), "MPSE"))
fluidRow(
shinydashboardPlus::box(
solidHeader = FALSE,
title = "Status summary",
background = NULL,
width = 12,
status = "danger",
fluidRow(
column(
width = 6,
descriptionBlock(
#number = paste0(mp_info()[5],"%"),
#numberColor = "red",
#numberIcon = icon("caret-down"),
header = mp_info()[1],
text = "Samples Size",
rightBorder = TRUE,
marginBottom = FALSE
)
),
column(
width = 6,
descriptionBlock(
#number = paste0(mp_info()[6],"%"),
#numberColor = "red",
#numberIcon = icon("caret-down"),
header = mp_info()[2],
text = "OTU Size",
rightBorder = FALSE,
marginBottom = FALSE
)
)
),
br(),
tags$b("Rare Abundance:"),
fluidRow(
column(
width = 6,
descriptionBlock(
number = paste0(mp_info()[5],"%"),
numberColor = "red",
numberIcon = icon("caret-down"),
header = mp_info()[3],
text = "Samples Size",
rightBorder = TRUE,
marginBottom = FALSE
)
),
column(
width = 6,
descriptionBlock(
number = paste0(mp_info()[6],"%"),
numberColor = "red",
numberIcon = icon("caret-down"),
header = mp_info()[4],
text = "OTU Size",
rightBorder = FALSE,
marginBottom = FALSE
)
)
)
)
)
})
# output$downloadAbu <- downloadHandler(
# filename = function(){
# if(input$rarefying){
# "RareAbundance.csv"
# }else{
# "Abundance.csv"
# }
# },
# content = function(file){
# req(inherits(mpse(), "MPSE"))
# if(input$rarefying){
# abun <- "RareAbundance"
# }else{
# abun <- "Abundance"
# }
#
# table <- mpse() %>% mp_extract_assays(.abundance = !!sym(abun))
# write.csv(table,
# file)
# })
# output$downloadTax <- downloadHandler(
# filename = function(){"Taxonomy_annotation.csv"},
# content = function(file){
# req(inherits(mpse(), "MPSE"))
# table <- mpse() %>% mp_extract_taxonomy
# write.csv(table,
# file,
# row.names = FALSE)
# })
return(mp_rare)
})
}