transfo rarefaction

panels/dataInput.R

@@ -145,7 +145,7 @@ observeEvent(input$okData, {
               d <- rarefy_even_depth(
                 d,
                 replace = FALSE,
-                rngseed = as.integer(Sys.time()),
+                rngseed = 314,
                 verbose = FALSE
               )
             }
@@ -284,7 +284,8 @@ transformSample <- function() {
       inputId = "transformFun",
       label = "Transform function : ",
       selected = NULL,
-      choices = c("Proportional Transformation" = "prop", 
+      choices = c("Rarefaction" = "rare",
+                  "Proportional Transformation" = "prop", 
                   "Square Root Transformation" = "sqrt", 
                   "Square Root Proportional Transformation" = "sqrtprop", 
                   "Centered Log-Ratio (CLR) Transformation" = "clr")
@@ -301,6 +302,7 @@ transformSample <- function() {
 output$transformFun <- renderText({
   validate(need(input$transformFun, ""))
   switch (input$transformFun,
+          "rare" = "data_rare <- rarefy_even_depth(data, rngseed = 314, replace = TRUE)",
           "prop" = paste("count_to_prop <- function(x) {return( x / sum(x) )}", 
                          "data_prop <- transform_sample_counts(data, count_to_prop)",
                          sep = "\n"),
@@ -329,6 +331,9 @@ observeEvent(input$transformData, {
     shinyWidgets::updateSwitchInput(session = session, inputId = "useTransf", value = FALSE)
     try(
       switch (input$transformFun,
+              "rare" = {
+                transform_physeq(rarefy_even_depth(select_physeq(), rngseed = 314, replace = TRUE))
+                },
               "prop" = {
                 count_to_prop <- function(x) {return( x / sum(x) )}
                 transform_physeq(transform_sample_counts(select_physeq(), count_to_prop))