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taxa_composition_sample.R
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taxa_composition_sample_ui <- function(id) {
ns <- NS(id)
res <- div(
#class = "tab-body",
fluidRow(
column(3,
shinydashboardPlus::box(
width = NULL,
collapsible = TRUE,
title = "Taxonomy composition Analysis",
status = "warning",
p("Click below to compute microbial abundance at each level. It's a time-consuming process, a single calculation should suffice."),
div(
style = "text-align:center; padding-top:10px;",
actionBttn(
ns("btn"),
"Calculating Abundance",
style = "jelly",
color = "warning"
)
)#close div
),
tabBox(width = NULL,
tabPanel(h5("Graphics Options"),
fluidRow(
column(6,
pickerInput(ns("level"),
"Taxonomic level:",
choices = NULL)
),
column(6,
pickerInput(ns("feature"),
"Sort by:",
NULL,
options = pickerOptions(liveSearch=T)) %>%
shinyInput_label_embed(
icon("circle-question") %>%
bs_embed_tooltip(title = "Sort according to the selected species.")
),
)
),
fluidRow(
column(6,
pickerInput(ns("group"),
"Group",
NULL,
options = pickerOptions(noneSelectedText = "NULL"))
),
column(6,
selectInput(inputId = ns('geom'),
label = 'Plot style',
choices = c('bar' = "bar",
"flowbar" = "flowbar")),
)
),
numericInput(ns("topn"), "Top most abundant:", value = 10),
tags$b("Whether to show:"),
prettyCheckbox(
inputId = ns("Samples_names"),
label = "Sample names",
value = FALSE,
status = "danger",
shape = "curve"
)
),#close tabPanel
tabPanel(h5("Download"),
fluidRow(
column(width = 6,
style=list("padding-right: 5px;"),
numericInput(ns("width_slider"), "Width:", 10,1, 20)
),
column(width = 6,
style=list("padding-left: 5px;"),
numericInput(ns("height_slider"), "Height:", 8, 1, 20)
)
),
fluidRow(
column(width = 6,
style=list("padding-right: 5px;"),
selectInput(inputId = ns('extPlot'),
label = 'Output format',
choices = c('PDF' = '.pdf',"PNG" = '.png','TIFF'='.tiff',"SVG" = '.svg')
),
),
column(width = 6,
style=list("padding-left: 5px;"),
numericInput(ns("dpi"), "DPI:", 300, 100, 600)
)
),
fluidRow(
column(width = 6,
downloadButton(ns("downloadPlot"), "Download Plot")),
column(width = 6,
downloadButton(ns("downloadTable"), "Download Table"))
)
)
),
shinydashboard::box(
title = "Example Plot",
width = NULL,
img(src="taxa_composition_samples.png",
align = "center",
width = "100%")
)
),
column(9,
plotOutput(ns("message"),height = "30px"),
jqui_resizable(
plotOutput(ns("taxa_composition_plot"), width = '900px', height = '600px'),
operation = c("enable", "disable", "destroy", "save", "load"),
options = list(
minHeight = 300, maxHeight = 900,
minWidth = 300, maxWidth = 1200
)
)#close jqui_resizable
)#close column
)
)
return(res)
}
taxa_composition_sample_mod <- function(id, mpse) {
moduleServer(
id,
function(input, output, session) {
ns <- session$ns
observe({
req(inherits(mpse, "MPSE"))
lev <- sapply(mp_extract_sample(mpse), function(n) length(unique(n)))
group <- names(lev[lev > 1])
group <- c("NULL",group)
updatePickerInput(session, "group", choices = group,
selected = "NULL")
taxa <- names(mp_extract_taxonomy(mpse))[-1]
updatePickerInput(session, "level", choices = taxa,
selected = taxa[3])
})
observe({
req(inherits(mpse, "MPSE"), input$level)
updatePickerInput(session, "feature",
choices = unique(mp_extract_taxonomy(mpse)[[input$level]])
)
})
mp_composition_sample <- eventReactive(input$btn, {
req(inherits(mpse, "MPSE"))
mp_composition_sample <- mpse %>%
mp_cal_abundance(.abundance = RareAbundance, action = "add")
return(mp_composition_sample)
})
p_taxa_composition <- reactive({
req(mp_composition_sample())
# level <- isolate({input$level})
# topn <- isolate({input$topn})
# feature <- isolate({input$feature})
# group <- isolate({input$group})
#plot
if(input$group == "NULL") {
p <- mp_composition_sample() %>%
mp_plot_abundance(.abundance=RareAbundance,
.group= NULL,
taxa.class = !!sym(input$level),
topn = input$topn,
force = TRUE,
geom = input$geom) +
theme(
axis.text.y = element_text(size = 16),
text = element_text(size = 18),
legend.text = element_text(size = 16)
)
}else{
p <- mp_composition_sample() %>%
mp_plot_abundance(.abundance=RareAbundance,
.group= !!sym(input$group),
taxa.class = !!sym(input$level),
topn = input$topn,
force = TRUE,
geom = input$geom) +
theme(
axis.text.y = element_text(size = 16),
text = element_text(size = 18),
legend.text = element_text(size = 16)
)
}
if(!input$Samples_names){
p <- p + theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank())
}
p_resort <- resort_p(p, input$feature)
return(p_resort)
})
output$message <- renderPlot({
req(p_taxa_composition())
feature <- isolate({input$feature})
data <- p_taxa_composition()$data
tax_names <- data[[1]] %>% levels
validate(
need(feature %in% tax_names, "The selected taxonomy belongs to the 'Others' category and cannot be sorted."
)#close need
)#close validate
})
output$taxa_composition_plot <- renderPlot({
req(p_taxa_composition())
p_taxa_composition()
})
output$downloadPlot <- downloadHandler(
filename = function(){
paste("taxa_composition_Sample", input$extPlot, sep='')},
content = function(file){
req(p_taxa_composition())
ggsave(file,
plot = p_taxa_composition(),
width = input$width_slider,
height = input$height_slider,
dpi = input$dpi)
})
output$downloadTable <- downloadHandler(
filename = function(){ "taxa_composition_Data.csv" },
content = function(file){
req(p_taxa_composition())
table <- p_taxa_composition()$data
n <- names(table)[sapply(table, class) == "list"]
write.csv(table %>% select(-c(n)),
file,
row.names = FALSE)
})
}
)
}