add clr function

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MicEco
 Title: Various functions for microbial community data
-Version: 0.9.12
+Version: 0.9.13
 Authors@R: person("Jakob", "Russel", email = "[email protected]", role = c("aut", "cre"))
 Description: Collection of functions for microbiome analyses. E.g. fitting neutral models and standardized effect sizes of phylogenetic beta diversities, and much more.
 Depends: R (>= 3.2.5)

NAMESPACE

@@ -3,6 +3,7 @@
 export(UniFrac.multi)
 export(WdS.test)
 export(adonis_OmegaSq)
+export(clr)
 export(comdist.par)
 export(comdistnt.par)
 export(community_rrna)

R/clr.R

@@ -0,0 +1,33 @@
+#' CLR transformation of community matrix, with multiplicative zero replacement
+#'
+#' This function performs a CLR transformation on the input.
+#' Prior to transformation it does a multiplicative zero replacement, which adds a pseudocount, but corrects the non-zero abundances such that log-ratios between non-zero elements are unchanged after correction.
+#' @param mat A community matrix with features as rows
+#' @param delta The pseudocount to exchange zeroes with. Zero-correction is multiplicative such that the log-ratios between any entirely non-zero features will not be affected by the pseudocount. 
+#' @keywords clr pseudocount
+#' @return CLR transformed community matrix
+#' @export
+
+clr <- function(mat, delta=1){
+
+  # Zero correction
+  mat_zc <- apply(mat, 2, function(y) sapply(y,function(x) ifelse(x==0,delta,(1-(sum(y==0)*delta)/sum(y))*x)))
+
+  if(any(mat_zc <= 0)) stop("Community matrix should only contain positive values")
+
+  # CLR transformation
+  gm_mean = function(x){
+    if(any(x < 0, na.rm = TRUE)){
+      stop("Negative values not allowed")
+    }
+    exp(mean(log(x)))
+  }
+
+  mat_gm <- apply(mat_zc,2,function(y) gm_mean(y))
+  mat_log <- t(log(t(mat_zc)/mat_gm))
+
+  rownames(mat_log) <- rownames(mat)
+  colnames(mat_log) <- colnames(mat)
+
+  return(mat_log)
+}

README.md

@@ -40,6 +40,10 @@ Rarefaction curve (theoretical and fast) from a phyloseq object. Output ready fo
 Clean tax_table such that NAs are replaced with names of the most specific known taxonomy prefixed with the rank.
 
 ## Miscellaneous functions
+#### clr
+
+CLR transformation of community matrix, with multiplicative zero replacement
+
 #### adonis_OmegaSq
 
 Calculate the unbiased effect size estimation (partial) omega-squared for adonis (PERMANOVA) models