fix_gsva_result.R

#' Sort the results of a gsva() call so that the
#' pathway activation always correlates positively
#' on average with the gene set listed
#' @param g Result of call to gsva() (pathway x cell)
#' @param genesets List of genes corresponding to genesets of g
#' @param sce A SingleCellExperiment with a logcounts assay
fix_gsva_direction <- function(g, genesets, sce) {
  stopifnot(nrow(g) == length(genesets))
  
  genesets <- lapply(genesets, intersect, rownames(sce))
  
  signs <- sapply(seq_along(genesets), function(i) {
    gg <- g[i,]
    cors <- apply(
      logcounts(sce)[genesets[[i]],],
      1,
      cor,
      gg
    )
    sign(mean(cors, na.rm=TRUE))
  })
  signs * g
}