diff --git a/internals.R b/internals.R
index 2327b09d98e00c2c94b96341a688e86976b0a088..5dde6e6e5fc3babbf71a05f9789d6fa7c60a94ca 100644
--- a/internals.R
+++ b/internals.R
@@ -103,14 +103,3 @@ beautifulTable <- function(data) {
height = "auto"
)
}
-
-collapsedBox <- function(data, title = title) {
- box(
- title = title,
- width = NULL,
- status = "primary",
- collapsible = TRUE,
- collapsed = TRUE,
- data
- )
-}
diff --git a/panels/Summary-server.R b/panels/Summary-server.R
index b58a783972604f52014b896b3c5815d7364d7387..648b33a8fc7140f0825661c2c2f3fe5f3a72ed5e 100644
--- a/panels/Summary-server.R
+++ b/panels/Summary-server.R
@@ -7,68 +7,3 @@ output$phyloseqPrint <- renderPrint({
)
physeq()
})
-
-output$otuTable <- renderUI({
- validate(need(physeq(), ""))
- collapsedBox(
- beautifulTable(data.frame(OTU = taxa_names(physeq()), otu_table(physeq()))),
- title = "OTU table"
- )
-})
-
-output$glomOtuTable <- renderUI({
- validate(need(physeq(), ""))
- box(
- title = "Agglomerate OTU table",
- width = NULL,
- status = "primary",
- collapsible = TRUE,
- collapsed = TRUE,
- radioButtons("glomRank",
- label = "Taxonomic rank : ",
- choices = rank_names(physeq()),
- inline = TRUE),
- DT::dataTableOutput("tableGlom")
- )
-})
-
-output$taxTable <- renderUI({
- validate(need(physeq(), ""))
- collapsedBox(
- beautifulTable(data.frame(OTU = taxa_names(physeq()), tax_table(physeq()))),
- title = "Taxonomy table"
- )
-})
-
-output$sampleDataTable <- renderUI({
- validate(need(physeq(), ""))
- collapsedBox(
- beautifulTable(data.frame(SAMPLE = sample_names(physeq()), sample_data(physeq()))),
- title = "Sample data table"
- )
-})
-
-output$sampleDataType <- renderUI({
- validate(need(sample_data(physeq(), errorIfNULL = FALSE), ""))
- collapsedBox(renderTable({
- (sapply(sample_data(physeq()), class))
- }, rownames = TRUE, colnames = FALSE),
- title = "Class of sample data")
-})
-
-output$tableGlom <- DT::renderDataTable(server = FALSE, {
- Glom <- tax_glom(physeq(), input$glomRank, NArm = FALSE)
- taxTableGlom <- Glom %>%
- tax_table() %>%
- as.data.frame(stringsAsFactors = FALSE) %>%
- dplyr::select(1:input$glomRank) %>%
- tibble::rownames_to_column()
- otuTableGlom <- Glom %>%
- otu_table() %>%
- as.data.frame(stringsAsFactors = FALSE) %>%
- tibble::rownames_to_column()
- joinGlom <-
- dplyr::left_join(taxTableGlom, otuTableGlom, by = "rowname") %>%
- dplyr::select(-rowname)
- beautifulTable(joinGlom)
-})
diff --git a/panels/Summary-ui.R b/panels/Summary-ui.R
index 1d1d4b4e03e821d79d3934285638bc4ea2084485..460c1ca213e2e788f5bd87f80f4a0d93557d2236 100644
--- a/panels/Summary-ui.R
+++ b/panels/Summary-ui.R
@@ -1,12 +1,9 @@
-Summary <- div(verbatimTextOutput("phyloseqPrint"),
- uiOutput("otuTable"),
- uiOutput("glomOtuTable"),
- uiOutput("taxTable"),
- uiOutput("sampleDataTable"),
- uiOutput("sampleDataType"),
- tags$footer("Questions, problems or comments regarding this application should be sent to ",
- a(href = "mailto:cedric.midoux@inrae.fr?subject=[Easy16S]", "cedric.midoux@inrae.fr"),
- align = "center",
- style = "position:absolute;bottom: 0;width: 100%;color: grey;padding: 10px;# background-color: white;z-index: 1000;"
- )
- )
+Summary <- fluidPage(
+ withLoader(verbatimTextOutput("phyloseqPrint")),
+ tags$footer(
+ "Questions, problems or comments regarding this application should be sent to ",
+ a(href = "mailto:cedric.midoux@inrae.fr?subject=[Easy16S]", "cedric.midoux@inrae.fr"),
+ align = "center",
+ style = "position:absolute;bottom: 0;width: 100%;color: grey;padding: 10px;# background-color: white;z-index: 1000;"
+ )
+)
diff --git a/panels/table-server.R b/panels/table-server.R
new file mode 100644
index 0000000000000000000000000000000000000000..12a207390b80452c8ce3a64020538364783502b9
--- /dev/null
+++ b/panels/table-server.R
@@ -0,0 +1,67 @@
+output$otuTable <- renderUI({
+ validate(need(physeq(), "Requires an abundance dataset"))
+ box(
+ title = "OTU table",
+ width = NULL,
+ status = "primary",
+ beautifulTable(tibble::rownames_to_column(as.data.frame(otu_table(physeq())), var = "OTU"))
+ )
+})
+
+output$taxTable <- renderUI({
+ validate(need(physeq(), "Requires an abundance dataset"))
+ box(
+ title = "Taxonomy table",
+ width = NULL,
+ status = "primary",
+ beautifulTable(tibble::rownames_to_column(as.data.frame(tax_table(physeq())), var = "OTU"))
+ )
+})
+
+output$glomTable <- renderUI({
+ validate(need(physeq(), "Requires an abundance dataset"))
+ box(
+ title = "Agglomerate OTU table",
+ width = NULL,
+ status = "primary",
+ radioButtons("glomRank",
+ label = "Taxonomic rank : ",
+ choices = rank_names(physeq()),
+ inline = TRUE),
+ withLoader(dataTableOutput("tableGlom"))
+ )
+})
+
+output$tableGlom <- renderDataTable({
+ Glom <- tax_glom(physeq(), input$glomRank, NArm = FALSE)
+ taxTableGlom <- Glom %>%
+ tax_table() %>%
+ as.data.frame(stringsAsFactors = FALSE) %>%
+ dplyr::select(1:input$glomRank) %>%
+ tibble::rownames_to_column()
+ otuTableGlom <- Glom %>%
+ otu_table() %>%
+ as.data.frame(stringsAsFactors = FALSE) %>%
+ tibble::rownames_to_column()
+ joinGlom <- dplyr::left_join(taxTableGlom, otuTableGlom, by = "rowname") %>%
+ dplyr::select(-rowname)
+ beautifulTable(joinGlom)
+})
+
+output$sampleTable <- renderUI({
+ validate(need(physeq(), "Requires an abundance dataset"))
+ box(
+ title = "Sample data table",
+ width = NULL,
+ status = "primary",
+ beautifulTable(tibble::rownames_to_column(as.data.frame(sample_data(physeq())), var = "SAMPLE")),
+ box(
+ title = "Class of sample data",
+ width = NULL,
+ status = "primary",
+ collapsible = TRUE,
+ collapsed = TRUE,
+ renderTable({(sapply(sample_data(physeq()), class))}, rownames = TRUE, colnames = FALSE)
+ )
+ )
+})
diff --git a/panels/table-ui.R b/panels/table-ui.R
new file mode 100644
index 0000000000000000000000000000000000000000..8d3b169bb2a40fe31959222f8ab87413fb856cfb
--- /dev/null
+++ b/panels/table-ui.R
@@ -0,0 +1,4 @@
+otuTable <- fluidPage(withLoader(uiOutput("otuTable")))
+taxtable <- fluidPage(withLoader(uiOutput("taxTable")))
+glomTable <- fluidPage(withLoader(uiOutput("glomTable")))
+sampleTable <- fluidPage(withLoader(uiOutput("sampleTable")))
diff --git a/server.R b/server.R
index b02a5798096427b7c7ac8ceee4b61b55b10db1da..edf7ffb35179f4eda4c7f333fc0fb7050823be73 100644
--- a/server.R
+++ b/server.R
@@ -6,6 +6,7 @@ library(phyloseq)
library(phyloseq.extended)
library(ggplot2)
library(dplyr)
+library(DT)
library(magrittr)
library(factoextra)
@@ -15,6 +16,7 @@ shinyServer
source("internals.R")
source("panels/dataInput.R", local = TRUE)
source("panels/Summary-server.R", local = TRUE)
+ source("panels/table-server.R", local = TRUE)
source("panels/barplot-server.R", local = TRUE)
source("panels/heatmap-server.R", local = TRUE)
source("panels/rarefactionCurve-server.R", local = TRUE)
diff --git a/ui.R b/ui.R
index dd708fe950cf39095bd406c0236fa6e994c7b828..eb35c1b37955d513e4c627f537c9aff1a6f734a6 100644
--- a/ui.R
+++ b/ui.R
@@ -2,6 +2,7 @@ library(shinydashboard)
library(shinymeta)
library(shinycustomloader)
source("panels/Summary-ui.R", local = TRUE)
+source("panels/table-ui.R", local = TRUE)
source("panels/barplot-ui.R", local = TRUE)
source("panels/heatmap-ui.R", local = TRUE)
source("panels/rarefactionCurve-ui.R", local = TRUE)
@@ -28,7 +29,13 @@ dashboardHeader(title = "Easy16S"),
icon = icon("download"),
style = "width: 80% ; color: black ; background-color: gray90"),
sidebarMenu(
- menuItem("Summary", tabName = "Summary", icon = icon("table")),
+ menuItem("Summary", tabName = "Summary", icon = icon("dna")),
+ menuItem("Tables", icon = icon("table"),
+ menuSubItem("OTU table", tabName = "otuTable"),
+ menuSubItem("Taxonomy table", tabName = "taxtable"),
+ menuSubItem("Agglomerate OTU table", tabName = "glomTable"),
+ menuSubItem("Sample data table", tabName = "sampleTable")
+ ),
menuItem("Barplot", tabName = "barplot", icon = icon("chart-bar")),
menuItem("Heatmap", tabName = "heatmap", icon = icon("chess-board")),
menuItem("Rarefaction curves", tabName = "rarefactionCurve", icon = icon("chart-line")),
@@ -53,6 +60,10 @@ dashboardHeader(title = "Easy16S"),
dashboardBody(
tabItems(
tabItem(tabName = "Summary", Summary),
+ tabItem(tabName = "otuTable", otuTable),
+ tabItem(tabName = "taxtable", taxtable),
+ tabItem(tabName = "glomTable", glomTable),
+ tabItem(tabName = "sampleTable", sampleTable),
tabItem(tabName = "barplot", barplot),
tabItem(tabName = "heatmap", heatmap),
tabItem(tabName = "rarefactionCurve", rarefactionCurve),