@@ -185,6 +185,7 @@ export("oncoPrint")

 export("order.comb_mat")

 export("packLegend")

 export("pindex")

+export("restore_matrix")

 export("rowAnnotation")

 export("row_anno_barplot")

 export("row_anno_boxplot")

@@ -3,6 +3,9 @@ CHANGES in VERSION 1.99.6

 * adjust the size of heatmap annotations and add testing scripts

 * run multiple times k-means to get a consensus partition

 * `show_heatmap_legend` is set to FALSE if `rect_gp = gpar(type = "none")`

+* add `restore_matrix()`

+* add `row_names_centered`/`column_names_centered` arguments to `Heatmap()`

+* `gp` in `anno_text()` supports `fill` and `border`

 ========================

@@ -2000,11 +2000,31 @@ anno_text = function(x, which = c("column", "row"), gp = gpar(),

 	row_fun = function(index) {

 		n = length(index)

-		grid.text(value[index], location, (n - seq_along(index) + 0.5)/n, gp = subset_gp(gp, index), just = just, rot = rot)

+		gp = subset_gp(gp, index)

+		gp2 = gp

+        if("border" %in% names(gp2)) gp2$col = gp2$border

+        if("fill" %in% names(gp2)) {

+        	if(!"border" %in% names(gp2)) gp2$col = gp2$fill

+        }

+        if(any(c("border", "fill") %in% names(gp2))) {

+        	grid.rect(y = (n - seq_along(index) + 0.5)/n, height = 1/n, gp = gp2)

+        }

+        

+		grid.text(value[index], location, (n - seq_along(index) + 0.5)/n, gp = gp, just = just, rot = rot)

 	}

 	column_fun = function(index, k = NULL, N = NULL, vp_name = NULL) {

 		n = length(index)

-		grid.text(value[index], (seq_along(index) - 0.5)/n, location, gp = subset_gp(gp, index), just = just, rot = rot)

+		gp = subset_gp(gp, index)

+		gp2 = gp

+        if("border" %in% names(gp2)) gp2$col = gp2$border

+        if("fill" %in% names(gp2)) {

+        	if(!"border" %in% names(gp2)) gp2$col = gp2$fill

+        }

+        if(any(c("border", "fill") %in% names(gp2))) {

+        	grid.rect(x = (seq_along(index) - 0.5)/n, width = 1/n, gp = gp2)

+        }

+        

+		grid.text(value[index], (seq_along(index) - 0.5)/n, location, gp = gp, just = just, rot = rot)

 	}

 	if(which == "row") {

@@ -137,12 +137,14 @@ Heatmap = setClass("Heatmap",

 # -row_names_max_width Maximum width of row names viewport.

 # -row_names_gp Graphic parameters for row names.

 # -row_names_rot Rotation of row names.

+# -row_names_centered Should row names put centered?

 # -column_labels Optional column labels which are put as column names in the heatmap.

 # -column_names_side Should the column names be put on the top or bottom of the heatmap?

 # -column_names_max_height Maximum height of column names viewport.

 # -show_column_names Whether show column names.

 # -column_names_gp Graphic parameters for drawing text.

 # -column_names_rot Rotation of column names.

+# -column_names_centered Should column names put centered?

 # -top_annotation A `HeatmapAnnotation` object.

 # -bottom_annotation A `HeatmapAnnotation` object.

 # -left_annotation It should be specified by `rowAnnotation`.

@@ -242,12 +244,14 @@ Heatmap = function(matrix, col, name,

     row_names_max_width = unit(6, "cm"), 

     row_names_gp = gpar(fontsize = 12), 

     row_names_rot = 0,

+    row_names_centered = FALSE,

     column_labels = colnames(matrix),

     column_names_side = c("bottom", "top"), 

     show_column_names = TRUE, 

     column_names_max_height = unit(6, "cm"), 

     column_names_gp = gpar(fontsize = 12),

     column_names_rot = 90,

+    column_names_centered = FALSE,

     top_annotation = NULL,

     bottom_annotation = NULL,

@@ -257,10 +261,10 @@ Heatmap = function(matrix, col, name,

     km = 1, 

     split = NULL, 

     row_km = km,

-    row_km_repeats = 10,

+    row_km_repeats = 1,

     row_split = split,

     column_km = 1,

-    column_km_repeats = 10,

+    column_km_repeats = 1,

     column_split = NULL,

     gap = unit(1, "mm"),

     row_gap = unit(1, "mm"),

@@ -540,15 +544,22 @@ Heatmap = function(matrix, col, name,

     .Object@row_names_param$show = show_row_names

     .Object@row_names_param$gp = check_gp(row_names_gp)

     .Object@row_names_param$rot = row_names_rot

+    .Object@row_names_param$centered = row_names_centered

     .Object@row_names_param$max_width = row_names_max_width + unit(2, "mm")

     # we use anno_text to draw row/column names because it already takes care of text rotation

     if(show_row_names) {

         if(length(row_labels) != nrow(matrix)) {

             stop_wrap("Length of `row_labels` should be the same as the nrow of matrix.")

         }

-        row_names_anno = anno_text(row_labels, which = "row", gp = row_names_gp, rot = row_names_rot,

-            location = ifelse(.Object@row_names_param$side == "left", 1, 0), 

-            just = ifelse(.Object@row_names_param$side == "left", "right", "left"))

+        if(row_names_centered) {

+            row_names_anno = anno_text(row_labels, which = "row", gp = row_names_gp, rot = row_names_rot,

+                location = 0.5, 

+                just = "center")

+        } else {

+            row_names_anno = anno_text(row_labels, which = "row", gp = row_names_gp, rot = row_names_rot,

+                location = ifelse(.Object@row_names_param$side == "left", 1, 0), 

+                just = ifelse(.Object@row_names_param$side == "left", "right", "left"))

+        }

         .Object@row_names_param$anno = row_names_anno

     }

@@ -560,17 +571,24 @@ Heatmap = function(matrix, col, name,

     .Object@column_names_param$show = show_column_names

     .Object@column_names_param$gp = check_gp(column_names_gp)

     .Object@column_names_param$rot = column_names_rot

+    .Object@column_names_param$centered = column_names_centered

     .Object@column_names_param$max_height = column_names_max_height + unit(2, "mm")

     if(show_column_names) {

         if(length(column_labels) != ncol(matrix)) {

             stop_wrap("Length of `column_labels` should be the same as the ncol of matrix.")

         }

-        column_names_anno = anno_text(column_labels, which = "column", gp = column_names_gp, rot = column_names_rot,

-            location = ifelse(.Object@column_names_param$side == "top", 0, 1), 

-            just = ifelse(.Object@column_names_param$side == "top", 

-                     ifelse(.Object@column_names_param$rot >= 0, "left", "right"),

-                     ifelse(.Object@column_names_param$rot >= 0, "right", "left")

-                    ))

+        if(column_names_centered) {

+            column_names_anno = anno_text(column_labels, which = "column", gp = column_names_gp, rot = column_names_rot,

+            location = 0.5, 

+            just = "center")

+        } else {

+            column_names_anno = anno_text(column_labels, which = "column", gp = column_names_gp, rot = column_names_rot,

+                location = ifelse(.Object@column_names_param$side == "top", 0, 1), 

+                just = ifelse(.Object@column_names_param$side == "top", 

+                         ifelse(.Object@column_names_param$rot >= 0, "left", "right"),

+                         ifelse(.Object@column_names_param$rot >= 0, "right", "left")

+                        ))

+        }

         .Object@column_names_param$anno = column_names_anno

     }

@@ -1146,7 +1164,6 @@ make_cluster = function(object, which = c("row", "column")) {

         }

         meanmat = do.call("cbind", meanmat)

-        hc = hclust(dist(t(meanmat)))

         # if `reorder` is a vector, the slice dendrogram is reordered by the mean of reorder in each slice

         # or else, weighted by the mean of `meanmat`.

         if(length(reorder) > 1) {

@@ -1154,7 +1171,12 @@ make_cluster = function(object, which = c("row", "column")) {

         } else {

             weight = colMeans(meanmat)

         }

-        hc = as.hclust(reorder(as.dendrogram(hc), weight, mean))

+        if(cluster_slices) {

+            hc = hclust(dist(t(meanmat)))

+            hc = as.hclust(reorder(as.dendrogram(hc), weight, mean))

+        } else {

+            hc = list(order = order(weight))

+        }

         cl2 = numeric(length(cl))

         for(i in seq_along(hc$order)) {

@@ -430,9 +430,9 @@ setMethod(f = "draw_title",

     if(which == "row") {

         pushViewport(viewport(name = paste(object@name, "row_title", k, sep = "_"), clip = FALSE, ...))

-        if("fill" %in% names(gp)) {

-            grid.rect(gp = gpar(fill = gp$fill))

-        }

+        gp2 = gp

+        if("border" %in% names(gp2)) gp2$col = gp2$border

+        if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)

         if(side == "left") {

             grid.text(title, x = unit(1, "npc") - ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

         } else {

@@ -441,9 +441,9 @@ setMethod(f = "draw_title",

         upViewport()

     } else {

         pushViewport(viewport(name = paste(object@name, "column_title", k, sep = "_"), clip = FALSE, ...))

-        if("fill" %in% names(gp)) {

-            grid.rect(gp = gpar(fill = gp$fill))

-        }

+        gp2 = gp

+        if("border" %in% names(gp2)) gp2$col = gp2$border

+        if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)

         if(side == "top") {

             grid.text(title, y = ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

         } else {

@@ -73,7 +73,7 @@ default_col = function(x, main_matrix = FALSE) {

     } else if(is.numeric(x)) {

         if(main_matrix) {

             p = sum(x > 0)/sum(x != 0)

-            if(p > 0.3 & p < 0.7) {

+            if(p > 0.25 & p < 0.75) {

                 if(ht_opt$verbose) {

                     cat("This matrix has both negative and positive values, use a color mapping symmetric to zero\n")

                 }

@@ -721,6 +721,90 @@ pindex = function(m, i, j) {

     }

 }

+# == title

+# Restore the index vector to index matrix in layer_fun

+#

+# == param

+# -j Column indices directly from ``layer_fun``.

+# -i Row indices directly from ``layer_fun``.

+# -x Position on x-direction directly from ``layer_fun``.

+# -y Position on y-direction directly from ``layer_fun``.

+#

+# == details

+# The values that are sent to ``layer_fun`` are all vectors (for the vectorization

+# of the grid graphic functions), however, the heatmap slice where

+# ``layer_fun`` is applied to, is still represented by a matrix, thus, it would be

+# very convinient if all the arguments in ``layer_fun`` can be converted to the

+# sub-matrix for the current slice. Here, as shown in above example,

+# `restore_matrix` does the job. `restore_matrix` directly accepts the first

+# four argument in ``layer_fun`` and returns an index matrix, where rows and

+# columns correspond to the rows and columns in the current slice, from top to

+# bottom and from left to right. The values in the matrix are the natural order

+# of e.g. vector ``j`` in current slice.

+#

+# For following code:

+#

+#     Heatmap(small_mat, name = "mat", col = col_fun,

+#         row_km = 2, column_km = 2,

+#         layer_fun = function(j, i, x, y, w, h, fill) {

+#             ind_mat = restore_matrix(j, i, x, y)

+#             print(ind_mat)

+#         }

+#     )

+#

+# The first output which is for the top-left slice:

+# 

+#          [,1] [,2] [,3] [,4] [,5]

+#     [1,]    1    4    7   10   13

+#     [2,]    2    5    8   11   14

+#     [3,]    3    6    9   12   15

+#

+# As you see, this is a three-row and five-column index matrix where the first

+# row corresponds to the top row in the slice. The values in the matrix

+# correspond to the natural index (i.e. 1, 2, ...) in ``j``, ``i``, ``x``, ``y``,

+# ... in ``layer_fun``. Now, if we want to add values on the second column in the

+# top-left slice, the code which is put inside ``layer_fun`` would look like:

+#

+#     for(ind in ind_mat[, 2]) {

+#         grid.text(small_mat[i[ind], j[ind]], x[ind], y[ind], ...)

+#     }

+#

+# == example

+# set.seed(123)

+# mat = matrix(rnorm(81), nr = 9)

+# Heatmap(mat, row_km = 2, column_km = 2,

+#     layer_fun = function(j, i, x, y, width, height, fill) {

+#        ind_mat = restore_matrix(j, i, x, y)

+#        print(ind_mat)

+# })

+#

+# set.seed(123)

+# mat = matrix(round(rnorm(81), 2), nr = 9)

+# Heatmap(mat, row_km = 2, column_km = 2,

+#     layer_fun = function(j, i, x, y, width, height, fill) {

+#        ind_mat = restore_matrix(j, i, x, y)

+#        ind = unique(c(ind_mat[2, ], ind_mat[, 3]))

+#        grid.text(pindex(mat, i[ind], j[ind]), x[ind], y[ind])

+# })

+restore_matrix = function(j, i, x, y) {

+    x = as.numeric(x)

+    y = as.numeric(y)

+    od = order(x, rev(y))

+    ind = seq_along(i)

+    j = j[od]

+    i = i[od]

+    x = x[od]

+    y = y[od]

+    ind = ind[od]

+    

+    nr = length(unique(i))

+    nc = length(unique(j))

+    # I = matrix(i, nrow = nr, ncol = nc)

+    # J = matrix(j, nrow = nr, ncol = nc)

+    IND = matrix(ind, nrow = nr, ncol = nc)

+    return(IND)

+}

+

 unit_with_vp = function(..., vp = current.viewport()$name) {

     u = unit(...)

@@ -52,12 +52,14 @@ Heatmap(matrix, col, name,

     row_names_max_width = unit(6, "cm"),

     row_names_gp = gpar(fontsize = 12),

     row_names_rot = 0,

+    row_names_centered = FALSE,

     column_labels = colnames(matrix),

     column_names_side = c("bottom", "top"),

     show_column_names = TRUE,

     column_names_max_height = unit(6, "cm"),

     column_names_gp = gpar(fontsize = 12),

     column_names_rot = 90,

+    column_names_centered = FALSE,

     top_annotation = NULL,

     bottom_annotation = NULL,

@@ -67,10 +69,10 @@ Heatmap(matrix, col, name,

     km = 1,

     split = NULL,

     row_km = km,

-    row_km_repeats = 10,

+    row_km_repeats = 1,

     row_split = split,

     column_km = 1,

-    column_km_repeats = 10,

+    column_km_repeats = 1,

     column_split = NULL,

     gap = unit(1, "mm"),

     row_gap = unit(1, "mm"),

@@ -138,12 +140,14 @@ Heatmap(matrix, col, name,

   \item{row_names_max_width}{Maximum width of row names viewport.}

   \item{row_names_gp}{Graphic parameters for row names.}

   \item{row_names_rot}{Rotation of row names.}

+  \item{row_names_centered}{Should row names put centered?}

   \item{column_labels}{Optional column labels which are put as column names in the heatmap.}

   \item{column_names_side}{Should the column names be put on the top or bottom of the heatmap?}

   \item{column_names_max_height}{Maximum height of column names viewport.}

   \item{show_column_names}{Whether show column names.}

   \item{column_names_gp}{Graphic parameters for drawing text.}

   \item{column_names_rot}{Rotation of column names.}

+  \item{column_names_centered}{Should column names put centered?}

   \item{top_annotation}{A \code{\link{HeatmapAnnotation}} object.}

   \item{bottom_annotation}{A \code{\link{HeatmapAnnotation}} object.}

   \item{left_annotation}{It should be specified by \code{\link{rowAnnotation}}.}

new file mode 100644

@@ -0,0 +1,79 @@

+\name{restore_matrix}

+\alias{restore_matrix}

+\title{

+Restore the index vector to index matrix in layer_fun

+}

+\description{

+Restore the index vector to index matrix in layer_fun

+}

+\usage{

+restore_matrix(j, i, x, y)

+}

+\arguments{

+

+  \item{j}{Column indices directly from \code{layer_fun}.}

+  \item{i}{Row indices directly from \code{layer_fun}.}

+  \item{x}{Position on x-direction directly from \code{layer_fun}.}

+  \item{y}{Position on y-direction directly from \code{layer_fun}.}

+

+}

+\details{

+The values that are sent to \code{layer_fun} are all vectors (for the vectorization

+of the grid graphic functions), however, the heatmap slice where

+\code{layer_fun} is applied to, is still represented by a matrix, thus, it would be

+very convinient if all the arguments in \code{layer_fun} can be converted to the

+sub-matrix for the current slice. Here, as shown in above example,

+\code{\link{restore_matrix}} does the job. \code{\link{restore_matrix}} directly accepts the first

+four argument in \code{layer_fun} and returns an index matrix, where rows and

+columns correspond to the rows and columns in the current slice, from top to

+bottom and from left to right. The values in the matrix are the natural order

+of e.g. vector \code{j} in current slice.

+

+For following code:

+

+  \preformatted{

+    Heatmap(small_mat, name = "mat", col = col_fun,

+        row_km = 2, column_km = 2,

+        layer_fun = function(j, i, x, y, w, h, fill) \{

+            ind_mat = restore_matrix(j, i, x, y)

+            print(ind_mat)

+        \}

+    )  }

+

+The first output which is for the top-left slice:

+

+  \preformatted{

+         [,1] [,2] [,3] [,4] [,5]

+    [1,]    1    4    7   10   13

+    [2,]    2    5    8   11   14

+    [3,]    3    6    9   12   15  }

+

+As you see, this is a three-row and five-column index matrix where the first

+row corresponds to the top row in the slice. The values in the matrix

+correspond to the natural index (i.e. 1, 2, ...) in \code{j}, \code{i}, \code{x}, \code{y},

+... in \code{layer_fun}. Now, if we want to add values on the second column in the

+top-left slice, the code which is put inside \code{layer_fun} would look like:

+

+  \preformatted{

+    for(ind in ind_mat[, 2]) \{

+        grid.text(small_mat[i[ind], j[ind]], x[ind], y[ind], ...)

+    \}  }

+}

+\examples{

+set.seed(123)

+mat = matrix(rnorm(81), nr = 9)

+Heatmap(mat, row_km = 2, column_km = 2,

+    layer_fun = function(j, i, x, y, width, height, fill) {

+       ind_mat = restore_matrix(j, i, x, y)

+       print(ind_mat)

+})

+

+set.seed(123)

+mat = matrix(round(rnorm(81), 2), nr = 9)

+Heatmap(mat, row_km = 2, column_km = 2,

+    layer_fun = function(j, i, x, y, width, height, fill) {

+       ind_mat = restore_matrix(j, i, x, y)

+       ind = unique(c(ind_mat[2, ], ind_mat[, 3]))

+       grid.text(pindex(mat, i[ind], j[ind]), x[ind], y[ind])

+})

+}