@@ -18,6 +18,9 @@

 #' larger than this value. Default \code{1}

 #' @param fdrThreshold Only use DEGs with FDR value smaller than this value.

 #' Default \code{0.05}

+#' @param topN An integer. Only to plot this number of top markers for each

+#' cluster in maximum, in terms of log2FC value. Use \code{NULL} to cancel the

+#' top N subscription. Default \code{10}.

 #' @param orderBy The ordering method of the clusters on the splitted heatmap.

 #' Can be chosen from \code{"size"} or \code{"name"}, specified with vector of

 #' ordered unique cluster labels, or set as \code{NULL} for unsplitted heatmap.

@@ -55,7 +58,7 @@

 #' @author Yichen Wang

 #' @export

 plotMarkerDiffExp <- function(inSCE, useAssay = 'logcounts', orderBy = 'size',

-    log2fcThreshold = 1, fdrThreshold = 0.05, decreasing = TRUE,

+    log2fcThreshold = 1, fdrThreshold = 0.05, topN = 10, decreasing = TRUE,

     rowDataName = NULL, colDataName = NULL, featureAnnotations = NULL,

     cellAnnotations = NULL, featureAnnotationColor = NULL,

     cellAnnotationColor = NULL,

@@ -87,6 +90,10 @@ plotMarkerDiffExp <- function(inSCE, useAssay = 'logcounts', orderBy = 'size',

     if(!all(c("Gene", "Pvalue", "Log2_FC", "FDR") %in% colnames(degFull)[1:4])){

         stop('"findMarker" result cannot be interpreted properly')

     }

+    if(length(which(!degFull$Gene %in% rownames(inSCE))) > 0){

+      # Remove genes happen in deg table but not in sce. Weird.

+      degFull <- degFull[-which(!degFull$Gene %in% rownames(inSCE)),]

+    }

     if(!is.null(log2fcThreshold)){

         degFull <- degFull[degFull$Log2_FC > log2fcThreshold,]

     }

@@ -105,11 +112,23 @@ plotMarkerDiffExp <- function(inSCE, useAssay = 'logcounts', orderBy = 'size',

         toRemove <- which(deg.gix)[-toKeep]

         degFull <- degFull[-toRemove,]

     }

-    if(length(which(!degFull$Gene %in% rownames(inSCE))) > 0){

-      degFull <- degFull[-which(!degFull$Gene %in% rownames(inSCE)),]

+    clusterName <- colnames(degFull)[5]

+    selected <- character()

+    if (!is.null(topN)) {

+      for (c in unique(degFull[[clusterName]])) {

+        deg.cluster <- degFull[degFull[[clusterName]] == c,]

+        deg.cluster <- deg.cluster[order(deg.cluster$Log2_FC, decreasing = TRUE),]

+        if (dim(deg.cluster)[1] > topN) {

+          deg.cluster <- deg.cluster[1:topN,]

+        }

+        selected <- c(selected, deg.cluster$Gene)

+      }

+    } else {

+      selected <- degFull$Gene

     }

+    degFull <- degFull[degFull$Gene %in% selected,]

     inSCE <- inSCE[degFull$Gene,]

-    clusterName <- colnames(degFull)[5]

+

     z <- SummarizedExperiment::colData(inSCE)[[clusterName]]

     if(is.factor(z)){

         z.order <- levels(z)

@@ -10,6 +10,7 @@ plotMarkerDiffExp(

   orderBy = "size",

   log2fcThreshold = 1,

   fdrThreshold = 0.05,

+  topN = 10,

   decreasing = TRUE,

   rowDataName = NULL,

   colDataName = NULL,

@@ -39,6 +40,10 @@ larger than this value. Default \code{1}}

 \item{fdrThreshold}{Only use DEGs with FDR value smaller than this value.

 Default \code{0.05}}

+\item{topN}{An integer. Only to plot this number of top markers for each

+cluster in maximum, in terms of log2FC value. Use \code{NULL} to cancel the

+top N subscription. Default \code{10}.}

+

 \item{decreasing}{Order the cluster decreasingly. Default \code{TRUE}.}

 \item{rowDataName}{character. The column name(s) in \code{rowData} that need