R/create_labels_txt.R

In cytolab/cytoMEM: Marker Enrichment Modeling (MEM)

create.labels.txt <- function(MEM_vals_scale,
             display.thresh,
             heatmap_data) {
        posRownamesMatrix <- matrix()
        negRownamesMatrix <- matrix()
        for (i in seq_len(nrow(heatmap_data))) {
            #Get markers above threshold
            posMarkers <- MEM_vals_scale[i, ][MEM_vals_scale[i, ] >= display.thresh]
            negMarkers <- MEM_vals_scale[i, ][MEM_vals_scale[i, ] < 0 & abs(MEM_vals_scale[i, ]) >= display.thresh]
            #Order markers by abs(MEM)
            posMarkersOrdered <- posMarkers[order(posMarkers, decreasing = TRUE)]
            negMarkersOrdered <- negMarkers[order(abs(negMarkers), decreasing = TRUE)]
            #Get + or - sign for each corresponding marker
            posVector <- rep("+", length(posMarkers))
            negVector <- rep("-", length(negMarkers))
            if (length(posVector) == 0) {
                posVector <- rep("None", 1)
            }
            if (length(negVector) == 0) {
                negVector <- rep("None", 1)
            }
            #Put together character vectors for rownames
            posSignedVec <- as.matrix(paste(posVector, abs(round(
                posMarkersOrdered, 2
            )), sep = ""))
            posMarkersRanked <- as.matrix(names(posMarkersOrdered))
            posRownames <- t(paste(posMarkersRanked, posSignedVec, sep = ""))
            posRownamesMatrix[i] <- apply(posRownames, 1, paste, collapse = " ")
            negSignedVec <- as.matrix(paste(negVector, abs(round(
                negMarkersOrdered, 2
            )), sep = ""))
            negMarkersRanked <- as.matrix(names(negMarkersOrdered))
            negRownames <- t(paste(negMarkersRanked, negSignedVec, sep = ""))
            negRownamesMatrix[i] <- apply(negRownames, 1, paste, collapse = " ")
        }
        dot <- rawToChar(as.raw(149))
        new_rownames <- paste("\n","\n",
          row.names(MEM_vals_scale),
          ":","\n",
          '\U25B2',
          posRownamesMatrix,"\n",
          '\U25BC',
          negRownamesMatrix,sep =""
        )
        return(new_rownames)
    }