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merge_samples checks for single value before coercing to numeric #893

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merge_samples checks for single value before coercing to numeric #893

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21 changes: 9 additions & 12 deletions R/merge-methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -478,8 +478,10 @@ setMethod("merge_taxa", "taxonomyTable", function(x, eqtaxa, archetype=1L){
#' the number of samples in \code{x}.
#'
#' @param fun (Optional). The function that will be used to merge the values that
#' correspond to the same group for each variable. It must take a numeric vector
#' as first argument and return a single value. Default is \code{\link[base]{mean}}.
#' correspond to the same group for each variable. It must take a vector
#' as first argument and return a single value. Default is to propagate the single
#' value if all values are the same, and to otherwise coerce to numeric and call
#' \code{\link[base]{mean}}.
#' Note that this is (currently) ignored for the otu_table, where the equivalent
#' function is \code{\link[base]{sum}}, but evaluated via \code{\link[base]{rowsum}}
#' for efficiency.
Expand Down Expand Up @@ -518,7 +520,8 @@ setGeneric("merge_samples", function(x, group, fun=mean) standardGeneric("merge_
################################################################################
#' @aliases merge_samples,sample_data-method
#' @rdname merge_samples-methods
setMethod("merge_samples", signature("sample_data"), function(x, group, fun=mean){
setMethod("merge_samples", signature("sample_data"),
function(x, group, fun=function(v) ifelse(length(unique(v)) == 1, v[[1]], mean(as.numeric(v))) ){
x1 <- data.frame(x)

# Check class of group and modify if "character"
Expand All @@ -531,15 +534,8 @@ setMethod("merge_samples", signature("sample_data"), function(x, group, fun=mean
group <- factor(group)
}

# Remove any non-coercable columns.
# Philosophy is to keep as much as possible. If it is coercable at all, keep.
# Coerce all columns to numeric matrix
coercable <- sapply(x1, canCoerce, "numeric")
x2 <- sapply(x1[, coercable], as, "numeric")
rownames(x2) <- rownames(x1)

# Perform the aggregation.
outdf <- aggregate(x2, list(group), fun)
outdf <- aggregate(x1, list(group), fun)
# get rownames from the "group" column (always first)
# rownames(outdf) <- as.character(outdf[, 1])
rownames(outdf) <- levels(group)
Expand All @@ -566,7 +562,8 @@ setMethod("merge_samples", signature("otu_table"), function(x, group){
################################################################################
#' @aliases merge_samples,phyloseq-method
#' @rdname merge_samples-methods
setMethod("merge_samples", signature("phyloseq"), function(x, group, fun=mean){
setMethod("merge_samples", signature("phyloseq"),
function(x, group, fun=function(v) ifelse(length(unique(v)) == 1, v[[1]], mean(as.numeric(v))) ){

# Check if phyloseq object has a sample_data
if( !is.null(sample_data(x, FALSE)) ){
Expand Down