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subset rows and columns before row scaling fix #164 Also set annotation colors after subsetting

87875172 authored on 14/05/2019 15:22:17
Showing 2 changed files

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@@ -9,7 +9,7 @@
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 #'  NULL, no subsetting will be performed. Default NULL.
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 #' @param cellIx Integer vector. Select cells for display in heatmap. If NULL,
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 #'  no subsetting will be performed. Default NULL.
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-#' @param scaleRow Function; A function to scale each individual row. Set to
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+#' @param scaleRow Function. A function to scale each individual row. Set to
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 #'  NULL to disable. Occurs after normalization and log transformation. Defualt
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 #'  is 'scale' and thus will Z-score transform each row.
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 #' @param trim Numeric vector. Vector of length two that specifies the lower
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@@ -116,26 +116,6 @@ plotHeatmap <- function(counts,
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     colorScheme <- match.arg(colorScheme)
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-    if (!is.null(scaleRow)) {
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-        if (is.function(scaleRow)) {
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-            cn <- colnames(counts)
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-            counts <- t(base::apply(counts, 1, scaleRow))
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-            colnames(counts) <- cn
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-        } else {
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-            stop("'scaleRow' needs to be of class 'function'")
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-        }
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-    }
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-
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-    if (!is.null(trim)) {
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-        if (length(trim) != 2) {
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-            stop("'trim' should be a 2 element vector specifying the lower",
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-                " and upper boundaries")
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-        }
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-        trim <- sort(trim)
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-        counts[counts < trim[1]] <- trim[1]
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-        counts[counts > trim[2]] <- trim[2]
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-    }
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-
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     ## Create cell annotation
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     if (!is.null(annotationCell) & !is.null(z)) {
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         if (is.null(rownames(annotationCell))) {
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@@ -173,6 +153,29 @@ plotHeatmap <- function(counts,
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         annotationFeature <- NA
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     }
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+    ## Select subsets of features/cells
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+    if (!is.null(featureIx)) {
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+        counts <- counts[featureIx, , drop = FALSE]
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+        if (length(annotationFeature) > 1 ||
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+                (length(annotationFeature) == 1 & !is.na(annotationFeature))) {
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+            annotationFeature <- annotationFeature[featureIx, , drop = FALSE]
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+        }
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+        if (!is.null(y)) {
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+            y <- y[featureIx]
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+        }
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+    }
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+
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+    if (!is.null(cellIx)) {
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+        counts <- counts[, cellIx, drop = FALSE]
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+        if (length(annotationCell) > 1 ||
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+                (length(annotationCell) == 1 & !is.na(annotationCell))) {
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+            annotationCell <- annotationCell[cellIx, , drop = FALSE]
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+        }
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+        if (!is.null(z)) {
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+            z <- z[cellIx]
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+        }
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+    }
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+
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     ## Set annotation colors
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     if (!is.null(z)) {
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         K <- sort(unique(z))
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@@ -201,27 +204,25 @@ plotHeatmap <- function(counts,
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         }
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     }
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-    ## Select subsets of features/cells
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-    if (!is.null(featureIx)) {
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-        counts <- counts[featureIx, , drop = FALSE]
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-        if (length(annotationFeature) > 1 ||
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-                (length(annotationFeature) == 1 & !is.na(annotationFeature))) {
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-            annotationFeature <- annotationFeature[featureIx, , drop = FALSE]
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-        }
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-        if (!is.null(y)) {
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-            y <- y[featureIx]
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+    # scale indivisual rows by scaleRow
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+    if (!is.null(scaleRow)) {
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+        if (is.function(scaleRow)) {
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+            cn <- colnames(counts)
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+            counts <- t(base::apply(counts, 1, scaleRow))
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+            colnames(counts) <- cn
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+        } else {
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+            stop("'scaleRow' needs to be of class 'function'")
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         }
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     }
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-    if (!is.null(cellIx)) {
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-        counts <- counts[, cellIx, drop = FALSE]
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-        if (length(annotationCell) > 1 ||
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-                (length(annotationCell) == 1 & !is.na(annotationCell))) {
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-            annotationCell <- annotationCell[cellIx, , drop = FALSE]
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-        }
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-        if (!is.null(z)) {
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-            z <- z[cellIx]
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+    if (!is.null(trim)) {
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+        if (length(trim) != 2) {
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+            stop("'trim' should be a 2 element vector specifying the lower",
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+                " and upper boundaries")
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         }
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+        trim <- sort(trim)
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+        counts[counts < trim[1]] <- trim[1]
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+        counts[counts > trim[2]] <- trim[2]
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     }
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     ## Set color scheme and breaks
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@@ -244,7 +245,6 @@ plotHeatmap <- function(counts,
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                 seq(colorSchemeCenter + 1e-6, uBoundRange,
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                     length.out = colLen - round(colLen / 2)))
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         }
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-
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     } else {
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         # Sequential color scheme
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         if (is.null(col)) {
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@@ -25,7 +25,7 @@ features and columns represent cells. .}
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 \item{y}{Numeric vector. Denotes feature module labels.}
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-\item{scaleRow}{Function; A function to scale each individual row. Set to
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+\item{scaleRow}{Function. A function to scale each individual row. Set to
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 NULL to disable. Occurs after normalization and log transformation. Defualt
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 is 'scale' and thus will Z-score transform each row.}
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