From d69aa8f42209e0eae01d366d1971beb61ab8e7aa Mon Sep 17 00:00:00 2001
From: Midoux Cedric <cedric.midoux@irstea.fr>
Date: Tue, 21 Apr 2020 17:15:52 +0200
Subject: [PATCH] CLR transfo (retours OC)
---
panels/dataInput.R | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/panels/dataInput.R b/panels/dataInput.R
index 932f436..5a6a55b 100644
--- a/panels/dataInput.R
+++ b/panels/dataInput.R
@@ -300,13 +300,13 @@ output$transformFun <- renderText({
sep = "\n"),
"sqrt" = "data_sqrt <- transform_sample_counts(data, sqrt)",
"clr" = paste("gm_mean <- function(x, na.rm=TRUE) {",
- " exp(sum(log(x[x > 0 & !is.na(x)]), na.rm=na.rm) / length(x))",
- " }",
- "clr <- function(x, base=2) {",
- " x <- log((x / gm_mean(x)), base)",
- " x[!is.finite(x) | is.na(x)] <- 0.0",
- " return(x)",
+ " return(exp(mean(log(x), na.rm=na.rm)))",
"}",
+ "clr <- function(x, base=exp(1)) {",
+ " x <- x+1",
+ " x <- log(x/gm_mean(x), base)",
+ " return(x)",
+ "}",
"data_clr <- transform_sample_counts(data, clr)",
sep = "\n")
)
@@ -328,11 +328,11 @@ observeEvent(input$transformData, {
},
"clr" = {
gm_mean <- function(x, na.rm=TRUE) {
- exp(sum(log(x[x > 0 & !is.na(x)]), na.rm=na.rm) / length(x))
+ return(exp(mean(log(x), na.rm=na.rm)))
}
- clr <- function(x, base=2) {
- x <- log((x / gm_mean(x)), base)
- x[!is.finite(x) | is.na(x)] <- 0.0
+ clr <- function(x, base=exp(1)) {
+ x <- x+1
+ x <- log(x/gm_mean(x), base)
return(x)
}
physeq(transform_sample_counts(physeq(), clr))
--
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