R/summary.mORT.R

In massiveGST: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test

summary.mORT <-
function(object, cols_to_remove = "link", 
                         order_by = c("relevance", "odds_ratio", "log2_odds_ratio", "p.value", "BH.value", "bonferroni"), 
                         top = NULL, 
                         as.formattable = FALSE, ...) {
  
  alternative <- attr(object, "alternative")
  order_by <- match.arg(order_by)
  
  if(order_by == "relevance") object$order <- order(object$relevance, decreasing = TRUE)
  if(order_by == "odds_ratio") object$order <- order(object$NES, decreasing = TRUE)
  if(order_by == "log2_odds_ratio") object$order <- order(object$NES, decreasing = TRUE)
  if(order_by == "p.value") object$order <- order(object$p.value)
  if(order_by == "BH.value") object$order <- order(object$BH.value)
  if(order_by == "bonferroni") object$order <- order(object$B.value)
  
#  oorder <- switch (order_by,
#               relevance = order(x$relevance, decreasing = TRUE),
#               NES = order(x$NES, decreasing = TRUE),
#               p.value = order(x$p.value),
#               BH.value = order(x$BH.value),
#               bonferroni = order(x$B.value)
#  )
 
  tmp <- object[object$order,]
  
  tmp$log2_odds_ratio <- round(tmp$log2_odds_ratio, 4)
  tmp$odds_ratio <- round(tmp$odds_ratio, 4)
#  if(alternative == "two.sided") tmp$abs_log2_odds_ratio <- round(tmp$abs_log2_odds_ratio, 2)
  tmp$p.value <- format(tmp$p.value, digits = 2)
  tmp$BH.value <- format(tmp$BH.value, digits = 2)
  tmp$B.value <- format(tmp$B.value, digits = 2)
  
  cols_to_remove <- c(cols_to_remove, "order")
  
  if(order_by != "relevance") cols_to_remove <- c(cols_to_remove, "relevance")
  
  if(!is.null(cols_to_remove)) tmp <- tmp[, -which(colnames(tmp) %in% cols_to_remove)]
  
  if(!is.null(top) & is.numeric(top)) {
    top <- as.integer(top)
    above <- min(top, sum(tmp$log2_odds_ratio >= 0))
    below <- min(top, sum(tmp$log2_odds_ratio < 0))
    nnrow <- nrow(tmp)
    if(alternative == "two.sided") {
      top <- trunc(top/2)
      tmp <- tmp[c(1:above, (nnrow-below+1):nnrow),]
      } else 
        if(alternative == "greater") tmp <- tmp[1:above,] else 
          tmp <- tmp[(nnrow-below+1):nnrow,]
  }
  
#  if(!verbose) return(tmp)
  if(as.formattable) {
    colnames(tmp)[2] <- "universe\nsize" 
    colnames(tmp)[3] <- "geneList\nsize" 
    colnames(tmp)[4] <- "geneSet\nsize" 
    colnames(tmp)[5] <- "geneList in\ngeneSet" 
    colnames(tmp)[7] <- "log2\nodds_ratio" 
    formattable(tmp, 
    list(log2_odds_ratio = formatter("span", style = ~ style("color" = ifelse(log2_odds_ratio >= 0, "red", "green"))))) } else {
           class(tmp) <- class(tmp)[-1]
           return(tmp)
         }
  
}