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easy16S
Commit a949d8e1 authored by Midoux Cedric's avatar Midoux Cedric
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Table with agglomerate taxe but not DataTable formatting

parent 2f2009bb
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Showing with 77 additions and 50 deletions
server.R
View file @ a949d8e1
......@@ -17,7 +17,7 @@ shinyServer
return(x)
}
}
beautifulTable <- function(data) {
DT::datatable(
data = data,
......@@ -27,7 +27,7 @@ shinyServer
options = list(
dom = "lBtip",
pageLength = 10,
lengthMenu = list(c(10, 25, 50, 100, -1), list('10', '25', '50', '100', 'All')),
lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
buttons = list(
'colvis',
list(
......@@ -44,32 +44,31 @@ shinyServer
height = "auto"
)
}
source({
"https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/R/load-extra-functions.R"
})
source("internals.R")
data16S <- reactive({
## BIOM input
if (input$dataset == "input")
{
## Unhappy path
if (is.null(input$fileBiom))
return()
## Happy path
## Import biom
d <- .import_biom(input)
## Format tax table
tax_table(d) <- .format_tax_table(tax_table(d))
## import metadata and store it in phyloseq object
sample_data(d) <- .import_sample_data(input, d)
## Rarefy data
if (input$rareData) {
d <- rarefy_even_depth(
......@@ -81,29 +80,30 @@ shinyServer
}
return(d)
}
## Rdata input
if (input$dataset == "rdata")
{
## .import_from_rdata(input) ## does not work as a function for some reason
## Happy path
ne <- new.env() ## new env to store RData content and avoid border effects
ne <-
new.env() ## new env to store RData content and avoid border effects
if (!is.null(input$fileRData))
load(input$fileRData$datapath, envir = ne)
if (class(ne$data) == "phyloseq")
return(ne$data)
## Unhappy paths: everything else
return()
}
## Default case
load("demo/demo.RData")
return(get(input$dataset))
})
data <- reactiveValues()
{
observe({
......@@ -111,7 +111,7 @@ shinyServer
isolate(data <<- data16S())
})
}
output$downloadData <- {
downloadHandler(
filename = function() {
......@@ -122,7 +122,7 @@ shinyServer
}
)
}
output$downloadUI <- renderUI({
validate(need(data16S(), ""))
tags$div(
......@@ -131,15 +131,15 @@ shinyServer
downloadButton("downloadData", "Download", style = "color: black; background-color: gray90")
)
})
output$rarefactionMin <- renderText({
validate(need(input$fileBiom, ""),
need(input$dataset == "input", ""))
paste("(min sample =", format(min(sample_sums(data16S(
))), big.mark = " "), "reads)")
})
output$phyloseqPrint <- renderPrint({
validate(
need(
......@@ -149,7 +149,7 @@ shinyServer
)
data16S()
})
output$summaryTable <- renderUI({
validate(need(data16S(), ""))
box(
......@@ -169,11 +169,38 @@ shinyServer
#as.data.frame(sapply(sample_data(data16S()), class)),
beautifulTable(
data.frame(SAMPLE = sample_names(data16S()), sample_data(data16S()))
))
)),
tabPanel(
"agglomerate_taxa",
radioButtons(
"glomRank",
label = "Taxonomic rank : ",
choices = rank_names(data16S()),
inline = TRUE
),
dataTableOutput("tableGlom")
)
)
)
})
output$tableGlom <- renderDataTable({
Glom <- tax_glom(data16S(), input$glomRank)
taxTableGlom <- Glom %>%
tax_table() %>%
as.data.frame() %>%
dplyr::select(1:input$glomRank) %>%
tibble::rownames_to_column()
otuTableGlom <- Glom %>%
otu_table() %>%
as.data.frame() %>%
tibble::rownames_to_column()
joinGlom <-
dplyr::left_join(taxTableGlom, otuTableGlom, by = "rowname") %>%
dplyr::select(-rowname)
return(joinGlom)
})
output$histUI <- renderUI({
validate(need(data16S(), ""))
box(
......@@ -202,7 +229,7 @@ shinyServer
)
)
})
output$histo <- renderPlot({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -218,7 +245,7 @@ shinyServer
}
return(p)
})
output$histFocusUIfocusRank <- renderUI({
validate(need(data16S(), ""))
radioButtons(
......@@ -228,19 +255,19 @@ shinyServer
inline = TRUE
)
})
output$histFocusUIfocusTaxa <- renderUI({
validate(need(data16S(), ""))
selectInput(
"focusTaxa",
label = "Selected taxa : ",
choices = unique(as.vector(tax_table(data16S(
))[, input$focusRank])),
selected = TRUE
)
})
output$histFocusUIfocusNbTaxa <- renderUI({
validate(need(data16S(), ""))
sliderInput(
......@@ -285,7 +312,7 @@ shinyServer
}
return(p)
})
output$clustUI <- renderUI({
validate(need(data16S(), ""))
box(
......@@ -326,7 +353,7 @@ shinyServer
)
)
})
output$clust <- renderPlot({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -337,7 +364,7 @@ shinyServer
color = checkNull(input$clustCol)
)
})
output$richnessAUI <- renderUI({
validate(need(data16S(), ""))
box(
......@@ -398,7 +425,7 @@ shinyServer
)
)
})
output$richnessA <- renderPlot({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -420,7 +447,7 @@ shinyServer
}
return(p)
})
output$richnessATable <- renderUI({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -428,7 +455,7 @@ shinyServer
SAMPLE = sample_names(data16S()), round(estimate_richness(data16S()), digits = 2)
)))
})
output$richnessBUI <- renderUI({
box(
title = "Setting : " ,
......@@ -444,7 +471,7 @@ shinyServer
value = "Beta diversity heatmap")
)
})
output$richnessB <- renderPlot({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -477,7 +504,7 @@ shinyServer
)
return(p + scale_fill_gradient2())
})
output$networkBUI <- renderUI({
validate(need(data16S(), ""))
box(
......@@ -518,7 +545,7 @@ shinyServer
)
)
})
output$networkB <- renderPlot({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -539,7 +566,7 @@ shinyServer
)
return(p)
})
output$richnessBTable <- renderUI({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -549,7 +576,7 @@ shinyServer
), digits = 2)
)))
})
output$rarefactionCurve <- renderPlot({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -564,16 +591,16 @@ shinyServer
if (!is.null(checkNull(input$rarefactionGrid))) {
p <- p + facet_grid(paste(".", "~", input$rarefactionGrid))
}
if (input$rarefactionMin) {
p <-
p + geom_vline(xintercept = min(sample_sums(data16S())),
color = "gray60")
}
return(p + ggtitle(input$rarefactionTitle))
})
output$rarefactionCurveUI <- renderUI({
validate(need(data16S(), ""))
box(
......@@ -608,7 +635,7 @@ shinyServer
)
)
})
output$HeatmapUI <- renderUI({
validate(need(data16S(), ""))
box(
......@@ -667,7 +694,7 @@ shinyServer
)
)
})
output$Heatmap <- renderPlot({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -689,7 +716,7 @@ shinyServer
}
return(p)
})
output$treeUI <- renderUI({
validate(need(data16S(), ""))
box(
......@@ -728,7 +755,7 @@ shinyServer
)
)
})
output$tree <- renderPlot({
validate(
need(data16S(), "Requires an abundance dataset"),
......@@ -757,7 +784,7 @@ shinyServer
return(p)
}
})
output$acpUI <- renderUI({
validate(need(data16S(), ""))
box(
......@@ -821,7 +848,7 @@ shinyServer
)
)
})
output$acp <- renderPlot({
validate(
need(data16S(), "Requires an abundance dataset"),
......
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