@@ -9,7 +9,7 @@

 #'  NULL, no subsetting will be performed. Default NULL.

 #' @param cellIx Integer vector. Select cells for display in heatmap. If NULL,

 #'  no subsetting will be performed. Default NULL.

-#' @param scaleRow Function; A function to scale each individual row. Set to

+#' @param scaleRow Function. A function to scale each individual row. Set to

 #'  NULL to disable. Occurs after normalization and log transformation. Defualt

 #'  is 'scale' and thus will Z-score transform each row.

 #' @param trim Numeric vector. Vector of length two that specifies the lower

@@ -116,26 +116,6 @@ plotHeatmap <- function(counts,

     colorScheme <- match.arg(colorScheme)

-    if (!is.null(scaleRow)) {

-        if (is.function(scaleRow)) {

-            cn <- colnames(counts)

-            counts <- t(base::apply(counts, 1, scaleRow))

-            colnames(counts) <- cn

-        } else {

-            stop("'scaleRow' needs to be of class 'function'")

-        }

-    }

-

-    if (!is.null(trim)) {

-        if (length(trim) != 2) {

-            stop("'trim' should be a 2 element vector specifying the lower",

-                " and upper boundaries")

-        }

-        trim <- sort(trim)

-        counts[counts < trim[1]] <- trim[1]

-        counts[counts > trim[2]] <- trim[2]

-    }

-

     ## Create cell annotation

     if (!is.null(annotationCell) & !is.null(z)) {

         if (is.null(rownames(annotationCell))) {

@@ -173,6 +153,29 @@ plotHeatmap <- function(counts,

         annotationFeature <- NA

     }

+    ## Select subsets of features/cells

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

+        counts <- counts[featureIx, , drop = FALSE]

+        if (length(annotationFeature) > 1 ||

+                (length(annotationFeature) == 1 & !is.na(annotationFeature))) {

+            annotationFeature <- annotationFeature[featureIx, , drop = FALSE]

+        }

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

+            y <- y[featureIx]

+        }

+    }

+

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

+        counts <- counts[, cellIx, drop = FALSE]

+        if (length(annotationCell) > 1 ||

+                (length(annotationCell) == 1 & !is.na(annotationCell))) {

+            annotationCell <- annotationCell[cellIx, , drop = FALSE]

+        }

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

+            z <- z[cellIx]

+        }

+    }

+

     ## Set annotation colors

     if (!is.null(z)) {

         K <- sort(unique(z))

@@ -201,27 +204,25 @@ plotHeatmap <- function(counts,

         }

     }

-    ## Select subsets of features/cells

-    if (!is.null(featureIx)) {

-        counts <- counts[featureIx, , drop = FALSE]

-        if (length(annotationFeature) > 1 ||

-                (length(annotationFeature) == 1 & !is.na(annotationFeature))) {

-            annotationFeature <- annotationFeature[featureIx, , drop = FALSE]

-        }

-        if (!is.null(y)) {

-            y <- y[featureIx]

+    # scale indivisual rows by scaleRow

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

+        if (is.function(scaleRow)) {

+            cn <- colnames(counts)

+            counts <- t(base::apply(counts, 1, scaleRow))

+            colnames(counts) <- cn

+        } else {

+            stop("'scaleRow' needs to be of class 'function'")

         }

     }

-    if (!is.null(cellIx)) {

-        counts <- counts[, cellIx, drop = FALSE]

-        if (length(annotationCell) > 1 ||

-                (length(annotationCell) == 1 & !is.na(annotationCell))) {

-            annotationCell <- annotationCell[cellIx, , drop = FALSE]

-        }

-        if (!is.null(z)) {

-            z <- z[cellIx]

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

+        if (length(trim) != 2) {

+            stop("'trim' should be a 2 element vector specifying the lower",

+                " and upper boundaries")

         }

+        trim <- sort(trim)

+        counts[counts < trim[1]] <- trim[1]

+        counts[counts > trim[2]] <- trim[2]

     }

     ## Set color scheme and breaks

@@ -244,7 +245,6 @@ plotHeatmap <- function(counts,

                 seq(colorSchemeCenter + 1e-6, uBoundRange,

                     length.out = colLen - round(colLen / 2)))

         }

-

     } else {

         # Sequential color scheme

         if (is.null(col)) {

@@ -25,7 +25,7 @@ features and columns represent cells. .}

 \item{y}{Numeric vector. Denotes feature module labels.}

-\item{scaleRow}{Function; A function to scale each individual row. Set to

+\item{scaleRow}{Function. A function to scale each individual row. Set to

 NULL to disable. Occurs after normalization and log transformation. Defualt

 is 'scale' and thus will Z-score transform each row.}