sqrtprop

panels/dataInput.R

@@ -279,6 +279,7 @@ transformSample <- function() {
       choices = c("None" = "none", 
                   "Proportional Transformation" = "prop", 
                   "Square Root Transformation" = "sqrt", 
+                  "Square Root Proportional Transformation" = "sqrtprop", 
                   "Centered Log-Ratio (CLR) Transformation" = "clr")
     ),
     
@@ -299,6 +300,9 @@ output$transformFun <- renderText({
                          "data_prop <- transform_sample_counts(data, count_to_prop)",
                          sep = "\n"),
           "sqrt" = "data_sqrt <- transform_sample_counts(data, sqrt)",
+          "sqrtprop" = paste("count_to_sqrtprop <- function(x) {return(sqrt(x / sum(x)))}", 
+                         "data_sqrtprop <- transform_sample_counts(data, count_to_sqrtprop)",
+                         sep = "\n"),
           "clr" = paste("gm_mean <- function(x, na.rm=TRUE) {",
                         "  return(exp(mean(log(x), na.rm=na.rm)))",
                         "}",
@@ -327,6 +331,10 @@ observeEvent(input$transformData, {
               "sqrt" = {
                 physeq(transform_sample_counts(physeq(), sqrt))
               },
+              "sqrtprop" = {
+                count_to_sqrtprop <- function(x) {return(sqrt(x / sum(x)))}
+                physeq(transform_sample_counts(physeq(), count_to_sqrtprop))
+              },
               "clr" = {
                 gm_mean <- function(x, na.rm=TRUE) {
                   return(exp(mean(log(x), na.rm=na.rm)))