Commit e7c1cb5a authored by Sandra Derozier's avatar Sandra Derozier
Browse files

Help text & Download debug

parent 5c182bbe
......@@ -55,6 +55,10 @@ app_server <- function(input, output, session) {
data$affi <- extract_affiliation(affi, input$asv) %>% dplyr::distinct()
amb <- find_level(data$affi)
output$txt <- renderUI(HTML({paste("<p><b>", input$asv, "- ", nrow(data$affi) ,"conflicting affiliation, ambiguity at rank ", amb, "</b></p>")}))
output$help <- renderUI(HTML({paste("<cite>Select an affiliation by clicking on a row.<br/>",
"It is possible to change the affiliation by double clicking on a cell in the table.</cite>")}))
output$table <- DT::renderDT({data$affi},
selection = list(mode = 'single', selected = NULL, target = 'row'),
editable = TRUE)
......@@ -95,9 +99,7 @@ app_server <- function(input, output, session) {
## Skip ASV
observeEvent(input$skip, {
data$amb_otus <- setdiff(data$amb_otus, input$asv)
updateSelectInput(session, "asv",
label = "Select ASV",
choices = data$amb_otus,
......@@ -112,7 +114,7 @@ app_server <- function(input, output, session) {
},
content = function(con) {
## Update taxonomy of object phyloseq
phyloseq::tax_table(physeq)[rownames(affiliations$cleaned), ] <- affiliations$cleaned
phyloseq::tax_table(physeq)[rownames(data$cleaned), ] <- data$cleaned
## revert short OTU names back to original names
dict <- setNames(object = otu_dictionary$sequence,
nm = otu_dictionary$OTU)
......
......@@ -35,6 +35,8 @@ app_ui <- function() {
solidHeader = T,
htmlOutput("tmptxt"),
htmlOutput("txt"),
#HTML("<br/>"),
htmlOutput("help"),
HTML("<br/>"),
DT::DTOutput("table"),
#HTML("<br/>"),
......
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