Binary files a/.DS_Store and b/.DS_Store differ

@@ -1,7 +1,7 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Making Complex Heatmaps

-Version: 1.3.3

+Version: 1.4.0

 Date: 2015-8-25

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

@@ -1,5 +1,6 @@

 export(column_anno_histogram)

 export(anno_boxplot)

+exportMethods(column_order)

 export(ColorMapping)

 export(HeatmapAnnotation)

 export(column_anno_boxplot)

@@ -27,6 +28,7 @@ exportClasses(AdditiveUnit)

 export(AdditiveUnit)

 export(max_text_height)

 exportMethods(annotation_legend_size)

+exportMethods(row_order)

 export(AdditiveUnit)

 exportMethods(draw_heatmap_list)

 export(row_anno_density)

@@ -35,6 +37,7 @@ export(decorate_heatmap_body)

 exportMethods(draw_heatmap_legend)

 exportMethods(add_heatmap)

 export(anno_barplot)

+exportMethods(row_dend)

 export(row_anno_boxplot)

 export(max_text_width)

 export(decorate_row_title)

@@ -61,12 +64,14 @@ export(column_anno_density)

 exportClasses(Heatmap)

 export(Heatmap)

 exportMethods(draw_annotation_legend)

+exportMethods(column_dend)

 exportMethods(set_component_height)

 export(HeatmapList)

 exportMethods(draw_annotation)

 exportMethods(make_column_cluster)

 export(SingleAnnotation)

 export(row_anno_histogram)

+export(select_region)

 exportMethods(get_color_mapping_list)

 exportMethods(make_row_cluster)

 exportMethods(component_width)

@@ -1,3 +1,13 @@

+CHANGES in VERSION 1.3.4

+

+* returned value for `draw` method has been changes

+* add `row_order`, `column_order`, `row_dend` and `column_dend`

+  to extract orders and dendrograms after heatmap clustering

+* add `select_region` to interactively select sub region in the heatmap

+  and retrieve row/column index in the selected sub region.

+

+====================================

+

 CHANGES in VERSION 1.3.3

 * set `row_reorder` and `column_reorder` to FALSE by default in `Heatmap()`

@@ -7,6 +7,8 @@ setGeneric('set_component_height', function(object, ...) standardGeneric('set_co

 setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))

+

 setGeneric('draw_hclust', function(object, ...) standardGeneric('draw_hclust'))

 setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

@@ -25,10 +27,10 @@ setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

-

 setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))

+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

+

 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

 setGeneric('draw', function(object, ...) standardGeneric('draw'))

@@ -41,6 +43,12 @@ setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_co

 setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

+

 setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

+

 setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

+

+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))

@@ -160,7 +160,7 @@ Heatmap = setClass("Heatmap",

 # -column_order order of column. It makes it easy to adjust column order for both matrix and column annotations.

 # -row_names_side should the row names be put on the left or right of the heatmap?

 # -show_row_names whether show row names.

-# -row_reorder apply reordering on rows. The value can be a logical value or a vector which contains weight 

+# -row_hclust_reorder apply reordering on rows. The value can be a logical value or a vector which contains weight 

 #               which is used to reorder rows

 # -row_names_max_width maximum width of row names viewport. Because some times row names can be very long, it is not reasonable

 #                      to show them all.

@@ -168,7 +168,7 @@ Heatmap = setClass("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_reorder apply reordering on columns. The value can be a logical value or a vector which contains weight 

+# -column_hclust_reorder apply reordering on columns. The value can be a logical value or a vector which contains weight 

 #               which is used to reorder columns

 # -column_names_gp graphic parameters for drawing text.

 # -top_annotation a `HeatmapAnnotation` object which contains a list of annotations.

@@ -216,12 +216,12 @@ Heatmap = function(matrix, col, name, na_col = "grey", color_space = "LAB",

     cluster_rows = TRUE, clustering_distance_rows = "euclidean",

     clustering_method_rows = "complete", row_hclust_side = c("left", "right"),

     row_hclust_width = unit(10, "mm"), show_row_hclust = TRUE, 

-    row_reorder = FALSE,

+    row_hclust_reorder = FALSE,

     row_hclust_gp = gpar(), cluster_columns = TRUE, 

     clustering_distance_columns = "euclidean", clustering_method_columns = "complete",

     column_hclust_side = c("top", "bottom"), column_hclust_height = unit(10, "mm"), 

     show_column_hclust = TRUE, column_hclust_gp = gpar(), 

-    column_reorder = FALSE,

+    column_hclust_reorder = FALSE,

     row_order = NULL, column_order = NULL,

     row_names_side = c("right", "left"), show_row_names = TRUE, 

     row_names_max_width = unit(4, "cm"), row_names_gp = gpar(fontsize = 12), 

@@ -323,14 +323,14 @@ Heatmap = function(matrix, col, name, na_col = "grey", color_space = "LAB",

             cluster_rows = FALSE

             show_row_hclust = FALSE

         }

-        row_reorder = FALSE

+        row_hclust_reorder = FALSE

         if("clustering_distance_columns" %in% called_args) {

         } else if(inherits(cluster_columns, c("dendrogram", "hclust"))) {

         } else {

             cluster_columns = FALSE

             show_column_hclust = FALSE

         }

-        column_reorder = FALSE

+        column_hclust_reorder = FALSE

         km = 1

     }

     .Object@matrix = matrix

@@ -461,7 +461,7 @@ Heatmap = function(matrix, col, name, na_col = "grey", color_space = "LAB",

     .Object@row_hclust_param$width = row_hclust_width + unit(1, "mm")  # append the gap

     .Object@row_hclust_param$show = show_row_hclust

     .Object@row_hclust_param$gp = check_gp(row_hclust_gp)

-    .Object@row_hclust_param$reorder = row_reorder

+    .Object@row_hclust_param$reorder = row_hclust_reorder

     .Object@row_order_list = list() # default order

     if(is.null(row_order)) {

         .Object@row_order = seq_len(nrow(matrix))

@@ -495,7 +495,7 @@ Heatmap = function(matrix, col, name, na_col = "grey", color_space = "LAB",

     .Object@column_hclust_param$height = column_hclust_height + unit(1, "mm")  # append the gap

     .Object@column_hclust_param$show = show_column_hclust

     .Object@column_hclust_param$gp = check_gp(column_hclust_gp)

-    .Object@column_hclust_param$reorder = column_reorder

+    .Object@column_hclust_param$reorder = column_hclust_reorder

     if(is.null(column_order)) {

         .Object@column_order = seq_len(ncol(matrix))

     } else {

@@ -81,7 +81,8 @@ HeatmapList = setClass("HeatmapList",

             layout_annotation_legend_bottom_height = unit(0, "mm"),

             layout_index = matrix(nrow = 0, ncol = 2),

-            graphic_fun_list = list()

+            graphic_fun_list = list(),

+            initialized = FALSE

         )

     ),

     contains = "AdditiveUnit"

@@ -210,6 +211,10 @@ setMethod(f = "make_layout",

     row_hclust_side = c("original", "left", "right"),

     row_sub_title_side = c("original", "left", "right")) {

+    if(object@layout$initialized) {

+        return(object)

+    }

+

     n = length(object@ht_list)

     i_main = main_heatmap[1]

@@ -542,6 +547,8 @@ setMethod(f = "make_layout",

         }

     }

+    object@layout$initialized = TRUE

+

     return(object)

 })

@@ -607,23 +614,14 @@ setMethod(f = "draw",

     upViewport()

-    # return a list of orders

-    n = length(object@ht_list)

-    dend_list = vector("list", n)

-    names(dend_list) = sapply(object@ht_list, function(ht) ht@name)

+    .LAST_HT_LIST$object = object

-    for(i in seq_len(n)) {

-        dend_list[[i]] = list(row = NULL, column = NULL)

-        if(inherits(object@ht_list[[i]], "HeatmapAnnotation")) {

-        } else {

-            dend_list[[i]]$column = object@ht_list[[i]]@column_hclust

-            dend_list[[i]]$row = object@ht_list[[i]]@row_hclust_list

-        }

-    }

-    return(invisible(dend_list))

+    return(invisible(object))

 })

+.LAST_HT_LIST = new.env()

+

 # == title

 # Width of each heatmap list component

 #

@@ -28,6 +28,8 @@ decorate_heatmap_body = function(heatmap, code = {}, slice = 1) {

 	seekViewport(vp_name)

 	e = new.env(parent = parent.frame())

 	eval(substitute(code), envir = e)

+

+	seekViewport("global")

 }

 # == title

@@ -66,6 +68,8 @@ decorate_hclust = function(heatmap, code, slice = 1, which = c("column", "row"))

 	seekViewport(vp_name)

 	e = new.env(parent = parent.frame())

 	eval(substitute(code), envir = e)

+

+	seekViewport("global")

 }

 # == title

@@ -135,6 +139,7 @@ decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row"

 	seekViewport(vp_name)

 	e = new.env(parent = parent.frame())

 	eval(substitute(code), envir = e)

+	seekViewport("global")

 }

 # == title

@@ -200,6 +205,7 @@ decorate_title = function(heatmap, code, slice = 1, which = c("column", "row"))

 	seekViewport(vp_name)

 	e = new.env(parent = parent.frame())

 	eval(substitute(code), envir = e)

+	seekViewport("global")

 }

 # == title

@@ -279,5 +285,6 @@ decorate_annotation = function(annotation, code, slice = NULL) {

 	e = new.env(parent = parent.frame())

 	eval(substitute(code), envir = e)

+	seekViewport("global")

 }

new file mode 100644

@@ -0,0 +1,194 @@

+

+# == title

+# Get row order from a heatmap list

+#

+# == param

+# -object a `HeatmapList-class` object

+#

+# == value

+# A list contains row orders which correspond to the original matrix

+#

+setMethod(f = "row_order",

+	signature = "HeatmapList",

+	definition = function(object) {

+

+	object = make_layout(object)

+

+	n = length(object@ht_list)

+	for(i in seq_len(n)) {

+        if(inherits(object@ht_list[[i]], "Heatmap")) {

+        	lt = object@ht_list[[i]]@row_order_list

+        	names(lt) = object@ht_list[[i]]@row_title

+        	return(lt)

+        }

+    }

+

+    return(NULL)

+	

+})

+

+# == title

+# Get row order from a heatmap

+#

+# == param

+# -object a `Heatmap-class` object

+#

+# == value

+# A list contains row orders which correspond to the original matrix

+#

+setMethod(f = "row_order",

+	signature = "Heatmap",

+	definition = function(object) {

+

+	object = prepare(object)

+

+	lt = object@row_order_list

+	names(lt) = object@row_title

+	return(lt)

+	

+})

+

+# == title

+# Get column order from a heatmap list

+#

+# == param

+# -object a `HeatmapList-class` object

+#

+# == value

+# A list contains column orders which correspond every matrix

+#

+setMethod(f = "column_order",

+	signature = "HeatmapList",

+	definition = function(object) {

+

+	object = make_layout(object)

+

+    n = length(object@ht_list)

+    order_list = vector("list", n)

+    names(order_list) = sapply(object@ht_list, function(ht) ht@name)

+

+    for(i in seq_len(n)) {

+        if(inherits(object@ht_list[[i]], "HeatmapAnnotation")) {

+        } else {

+            order_list[[i]] = object@ht_list[[i]]@column_order

+        }

+    }

+

+    return(order_list)

+

+})

+

+# == title

+# Get column order from a heatmap list

+#

+# == param

+# -object a `Heatmap-class` object

+#

+# == value

+# A vector containing column orders

+#

+setMethod(f = "column_order",

+	signature = "Heatmap",

+	definition = function(object) {

+

+	object = prepare(object)

+

+	return(object@column_order)

+	

+})

+

+# == title

+# Get row dendrograms from a heatmap list

+#

+# == param

+# -object a `HeatmapList-class` object

+# 

+# == value

+# A list of dendrograms for which each dendrogram corresponds to a row slice

+#

+setMethod(f = "row_dend",

+	signature = "HeatmapList",

+	definition = function(object) {

+

+	object = make_layout(object)

+

+	n = length(object@ht_list)

+    for(i in seq_len(n)) {

+        if(inherits(object@ht_list[[i]], "Heatmap")) {

+        	lt = object@ht_list[[i]]@row_hclust_list

+        	names(lt) = object@ht_list[[i]]@row_title

+        	return(lt)

+        }

+    }

+

+    return(NULL)

+})

+

+# == title

+# Get row dendrograms from a heatmap

+#

+# == param

+# -object a `HeatmapList` object

+# 

+# == value

+# A list of dendrograms for which each dendrogram corresponds to a row slice

+#

+setMethod(f = "row_dend",

+	signature = "Heatmap",

+	definition = function(object) {

+

+	object = prepare(object)

+

+	lt = object@row_hclust_list

+	names(lt) = object@row_title

+	return(lt)

+})

+

+# == title

+# Get column dendrograms from a heatmap list

+#

+# == param

+# -object a `HeatmapList-class` object

+# 

+# == value

+# A list of dendrograms for which dendrogram corresponds to each matrix

+#

+setMethod(f = "column_dend",

+	signature = "HeatmapList",

+	definition = function(object) {

+

+	object = make_layout(object)

+

+	# return a list of orders

+    n = length(object@ht_list)

+    dend_list = vector("list", n)

+    names(dend_list) = sapply(object@ht_list, function(ht) ht@name)

+

+    for(i in seq_len(n)) {

+        if(inherits(object@ht_list[[i]], "HeatmapAnnotation")) {

+        } else {

+            dend_list[[i]] = object@ht_list[[i]]@column_hclust

+        }

+    }

+

+    return(dend_list)

+})

+

+# == title

+# Get column dendrograms from a heatmap

+#

+# == param

+# -object a `Heatmap-class` object

+# 

+# == value

+# A dendrogram object

+#

+setMethod(f = "column_dend",

+	signature = "Heatmap",

+	definition = function(object) {

+

+	object = prepare(object)

+

+	return(object@column_hclust)

+})

+

@@ -17,6 +17,7 @@

 # -row_barplot_width width of barplot annotation on rows. It should be a `grid::unit` object

 # -show_column_barplot whether show barplot annotation on columns

 # -column_barplot_height height of barplot annotatioin on columns. it should be a `grid::unit` object.

+# -remove_empty_columns if there is no alteration in that sample, whether remove it on the heatmap

 # -... pass to `Heatmap`

 #

 # == details

@@ -35,6 +36,7 @@ oncoPrint = function(mat, get_type = function(x) x,

 	pct_gp = gpar(), axis_gp = gpar(fontsize = 8), 

 	show_row_barplot = TRUE, row_barplot_width = unit(2, "cm"),

 	show_column_barplot = TRUE, column_barplot_height = unit(2, "cm"),

+	remove_empty_columns = TRUE,

 	...) {

 	# convert mat to mat_list

@@ -77,8 +79,10 @@ oncoPrint = function(mat, get_type = function(x) x,

 		arr[, , i] = mat_list[[i]]

 	}

-	l = rowSums(apply(arr, c(2, 3), sum)) > 0

-	arr = arr[, l, , drop = FALSE]

+	if(remove_empty_columns) {

+		l = rowSums(apply(arr, c(2, 3), sum)) > 0

+		arr = arr[, l, , drop = FALSE]

+	}

 	# validate alter_fun_list

 	if(is.null(alter_fun_list$background)) alter_fun_list$background = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "#CCCCCC", col = NA))

new file mode 100644

@@ -0,0 +1,152 @@

+

+# == title

+# Select a region in the heatmap

+#

+# == param

+# -mark whether show the rectangular selected region

+#

+# == details

+# Users can use mouse to click two positions on the heatmap, the function

+# will return the row index and column index for the selected region in the selected matrix.

+# 

+select_region = function(mark = FALSE) {

+

+	if(!interactive()) {

+		stop("`select()` can only be used under interactive mode.")

+	}

+

+	x = dev.cur()

+	if(! (names(x) %in% c("quartz", "X11", "windows", "JavaGD", "CairoX11", "CairoWin")) ) {

+		stop("Can not detect any interactive graphic device.")

+	}

+

+	seekViewport("main_heatmap_list")

+

+	cat("Click two positions on the heatmap:\n")

+	pos1 = grid.locator(unit = "mm")

+	cat("  x:", sprintf("%.1f", pos1$x), "mm, y:", sprintf("%.1f", pos1$y), "mm\n")

+	pos2 = grid.locator(unit = "mm")

+	cat("  x:", sprintf("%.1f", pos2$x), "mm, y:", sprintf("%.1f", pos2$y), "mm\n")

+

+	# pos1 is always at bottom left

+	# pos2 is always at top right

+	if(compare_width(pos1$x, pos2$x) > 0) {

+		tmp = pos2$x

+		pos2$x = pos1$x

+		pos1$x = tmp

+	}

+

+	if(compare_height(pos1$y, pos2$y) > 0) {

+		tmp = pos2$y

+		pos2$y = pos1$y

+		pos1$y = tmp

+	}

+

+	for(i in seq_along(.LAST_HT_LIST$object@ht_list)) {

+		if(inherits(.LAST_HT_LIST$object@ht_list[[i]], "Heatmap")) {

+			ht = .LAST_HT_LIST$object@ht_list[[i]]

+			ht_name = ht@name

+			

+			seekViewport(qq("heatmap_@{ht_name}", code.pattern = "@\\{CODE\\}"))

+			vp = current.viewport()

+

+			pos1_cp = list()

+			pos2_cp = list()

+

+			# relative to current heatmap body

+			pos1_cp$x = pos1$x - convertWidth(vp$x, "mm") - sum(component_width(ht, 1:3))

+			pos1_cp$y = pos1$y - convertHeight(vp$y, "mm") - sum(component_height(ht, 6:9))

+			pos2_cp$x = pos2$x - convertWidth(vp$x, "mm") - sum(component_width(ht, 1:3))

+			pos2_cp$y = pos2$y - convertHeight(vp$y, "mm") - sum(component_height(ht, 6:9))

+

+			pos1_cp$x = convertWidth(pos1_cp$x, "mm")

+			pos1_cp$y = convertHeight(pos1_cp$y, "mm")

+			pos2_cp$x = convertWidth(pos2_cp$x, "mm")

+			pos2_cp$y = convertHeight(pos2_cp$y, "mm")

+

+			for(i in seq_along(ht@row_order_list)) {

+				

+				pos1_cp2 = list()

+				pos2_cp2 = list()

+

+				seekViewport(qq("@{ht_name}_heatmap_body_@{i}"))

+				vp2 = current.viewport()

+				pos1_cp2$x = pos1_cp$x

+				pos1_cp2$y = pos1_cp$y - (vp2$y - vp2$height)

+				pos2_cp2$x = pos2_cp$x

+				pos2_cp2$y = pos2_cp$y - (vp2$y - vp2$height)

+

+				pos1_cp2$x = convertWidth(pos1_cp2$x, "mm")

+				pos1_cp2$y = convertHeight(pos1_cp2$y, "mm")

+				pos2_cp2$x = convertWidth(pos2_cp2$x, "mm")

+				pos2_cp2$y = convertHeight(pos2_cp2$y, "mm")

+			

+				# test whether two clicks are in one heatmap body

+				if(compare_width(pos1_cp2$x) < 0 || compare_height(pos1_cp2$y) < 0 ||

+				   compare_width(pos2_cp2$x) < 0 || compare_height(pos2_cp2$y) < 0 ||

+				   compare_width(pos1_cp2$x, vp2$width) > 0 || compare_width(pos2_cp2$x, vp2$width) > 0 ||

+				   compare_height(pos1_cp2$y, vp2$height) > 0 || compare_height(pos2_cp2$y, vp2$height) > 0) {

+					

+				} else {

+					# extract row index and column index

+					# be careful with row slices

+					ht_width = convertWidth(vp2$width, "mm")

+					ht_height = convertHeight(vp2$height, "mm")

+

+					res = list()

+

+					nc = length(ht@column_order)

+

+					x1 = ceiling(as.numeric(pos1_cp2$x) / as.numeric(ht_width) * nc)

+					x2 = ceiling(as.numeric(pos2_cp2$x) / as.numeric(ht_width) * nc)

+

+					res$column_order = ht@column_order[x1:x2]

+

+					nr = length(ht@row_order_list[[i]])

+

+					y1 = 1 +nr - ceiling(as.numeric(pos1_cp2$y) / as.numeric(ht_height) * nr)

+					y2 = 1 + nr - ceiling(as.numeric(pos2_cp2$y) / as.numeric(ht_height) * nr)

+

+					res$row_order = ht@row_order_list[[i]][y2:y1]

+

+					if(mark) {

+						grid.rect( (pos1_cp2$x + pos2_cp2$x)*0.5, (pos1_cp2$y + pos2_cp2$y)*0.5,

+							       abs_unit(pos2_cp2$x - pos1_cp2$x), abs_unit(pos2_cp2$y - pos1_cp2$y) )

+					}

+

+					return(res)

+				}

+			}

+		} else {

+			stop("Do not click into row annotation regions.\n")

+		}

+	}

+

+	cat("\nTwo clicks should be in one same heatmap (or slice) region.\n\n")

+	select_region()

+

+}

+

+compare_width = function(u1, u2 = unit(0, "mm")) {

+

+	u1 = convertWidth(u1, "mm", valueOnly = TRUE)

+	u2 = convertWidth(u2, "mm", valueOnly = TRUE)

+

+	ifelse(u1 > u2, 1, ifelse(u1 < u2, -1, 0))

+}

+

+

+compare_height = function(u1, u2 = unit(0, "mm")) {

+

+	u1 = convertHeight(u1, "mm", valueOnly = TRUE)

+	u2 = convertHeight(u2, "mm", valueOnly = TRUE)

+

+	ifelse(u1 > u2, 1, ifelse(u1 < u2, -1, 0))

+}

+

+abs_unit = function(u) {

+	if(compare_unit(u) < 0) u = -1*u

+	return(u)

+}

+

+

@@ -39,6 +39,7 @@ increase_color_mapping_index = function() {

     INDEX_ENV$I_COLOR_MAPPING = INDEX_ENV$I_COLOR_MAPPING + 1

 }

+

 # default colors for matrix or annotations

 # this function should be improved later

 default_col = function(x, main_matrix = FALSE) {

@@ -17,12 +17,12 @@ Heatmap(matrix, col, name, na_col = "grey", color_space = "LAB",

     cluster_rows = TRUE, clustering_distance_rows = "euclidean",

     clustering_method_rows = "complete", row_hclust_side = c("left", "right"),

     row_hclust_width = unit(10, "mm"), show_row_hclust = TRUE,

-    row_reorder = FALSE,

+    row_hclust_reorder = FALSE,

     row_hclust_gp = gpar(), cluster_columns = TRUE,

     clustering_distance_columns = "euclidean", clustering_method_columns = "complete",

     column_hclust_side = c("top", "bottom"), column_hclust_height = unit(10, "mm"),

     show_column_hclust = TRUE, column_hclust_gp = gpar(),

-    column_reorder = FALSE,

+    column_hclust_reorder = FALSE,

     row_order = NULL, column_order = NULL,

     row_names_side = c("right", "left"), show_row_names = TRUE,

     row_names_max_width = unit(4, "cm"), row_names_gp = gpar(fontsize = 12),

@@ -73,13 +73,13 @@ Heatmap(matrix, col, name, na_col = "grey", color_space = "LAB",

   \item{column_order}{order of column. It makes it easy to adjust column order for both matrix and column annotations.}

   \item{row_names_side}{should the row names be put on the left or right of the heatmap?}

   \item{show_row_names}{whether show row names.}

-  \item{row_reorder}{apply reordering on rows. The value can be a logical value or a vector which contains weight which is used to reorder rows}

+  \item{row_hclust_reorder}{apply reordering on rows. The value can be a logical value or a vector which contains weight which is used to reorder rows}

   \item{row_names_max_width}{maximum width of row names viewport. Because some times row names can be very long, it is not reasonableto show them all.}

   \item{row_names_gp}{graphic parameters for drawing text.}

   \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_reorder}{apply reordering on columns. The value can be a logical value or a vector which contains weight which is used to reorder columns}

+  \item{column_hclust_reorder}{apply reordering on columns. The value can be a logical value or a vector which contains weight which is used to reorder columns}

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

   \item{top_annotation}{a \code{\link{HeatmapAnnotation}} object which contains a list of annotations.}

   \item{top_annotation_height}{total height of the column annotations on the top.}

new file mode 100644

@@ -0,0 +1,19 @@

+\name{column_dend-Heatmap-method}

+\alias{column_dend,Heatmap-method}

+\title{

+Get column dendrograms from a heatmap

+}

+\description{

+Get column dendrograms from a heatmap

+}

+\usage{

+\S4method{column_dend}{Heatmap}(object)

+}

+\arguments{

+

+  \item{object}{a \code{\link{Heatmap-class}} object}

+

+}

+\value{

+A dendrogram object

+}

new file mode 100644

@@ -0,0 +1,19 @@

+\name{column_dend-HeatmapList-method}

+\alias{column_dend,HeatmapList-method}

+\title{

+Get column dendrograms from a heatmap list

+}

+\description{

+Get column dendrograms from a heatmap list

+}

+\usage{

+\S4method{column_dend}{HeatmapList}(object)

+}

+\arguments{

+

+  \item{object}{a \code{\link{HeatmapList-class}} object}

+

+}

+\value{

+A list of dendrograms for which dendrogram corresponds to each matrix

+}

new file mode 100644

@@ -0,0 +1,22 @@

+\name{column_dend-dispatch}

+\alias{column_dend}

+\title{

+Method dispatch page for column_dend

+}

+\description{

+Method dispatch page for \code{column_dend}.

+}

+\section{Dispatch}{

+\code{column_dend} can be dispatched on following classes:

+

+\itemize{

+\item \code{\link{column_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{column_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method

+}

+}

+\examples{

+# no example

+NULL

+

+

+}

new file mode 100644

@@ -0,0 +1,19 @@

+\name{column_order-Heatmap-method}

+\alias{column_order,Heatmap-method}

+\title{

+Get column order from a heatmap list

+}

+\description{

+Get column order from a heatmap list

+}

+\usage{

+\S4method{column_order}{Heatmap}(object)

+}

+\arguments{

+

+  \item{object}{a \code{\link{Heatmap-class}} object}

+

+}

+\value{

+A vector containing column orders

+}

new file mode 100644

@@ -0,0 +1,19 @@

+\name{column_order-HeatmapList-method}

+\alias{column_order,HeatmapList-method}

+\title{

+Get column order from a heatmap list

+}

+\description{

+Get column order from a heatmap list

+}

+\usage{

+\S4method{column_order}{HeatmapList}(object)

+}

+\arguments{

+

+  \item{object}{a \code{\link{HeatmapList-class}} object}

+

+}

+\value{

+A list contains column orders which correspond every matrix

+}

new file mode 100644

@@ -0,0 +1,22 @@

+\name{column_order-dispatch}

+\alias{column_order}

+\title{

+Method dispatch page for column_order

+}

+\description{

+Method dispatch page for \code{column_order}.

+}

+\section{Dispatch}{

+\code{column_order} can be dispatched on following classes:

+

+\itemize{

+\item \code{\link{column_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method

+}

+}

+\examples{

+# no example

+NULL

+

+

+}

@@ -12,6 +12,7 @@ oncoPrint(mat, get_type = function(x) x,

     pct_gp = gpar(), axis_gp = gpar(fontsize = 8),

     show_row_barplot = TRUE, row_barplot_width = unit(2, "cm"),

     show_column_barplot = TRUE, column_barplot_height = unit(2, "cm"),

+    remove_empty_columns = TRUE,

     ...)

 }

 \arguments{

@@ -27,6 +28,7 @@ oncoPrint(mat, get_type = function(x) x,

   \item{row_barplot_width}{width of barplot annotation on rows. It should be a \code{\link[grid]{unit}} object}

   \item{show_column_barplot}{whether show barplot annotation on columns}

   \item{column_barplot_height}{height of barplot annotatioin on columns. it should be a \code{\link[grid]{unit}} object.}

+  \item{remove_empty_columns}{if there is no alteration in that sample, whether remove it on the heatmap}

   \item{...}{pass to \code{\link{Heatmap}}}

 }

new file mode 100644

@@ -0,0 +1,19 @@

+\name{row_dend-Heatmap-method}

+\alias{row_dend,Heatmap-method}

+\title{

+Get row dendrograms from a heatmap

+}

+\description{

+Get row dendrograms from a heatmap

+}

+\usage{

+\S4method{row_dend}{Heatmap}(object)

+}

+\arguments{

+

+  \item{object}{a \code{\link{HeatmapList}} object}

+

+}

+\value{

+A list of dendrograms for which each dendrogram corresponds to a row slice

+}

new file mode 100644

@@ -0,0 +1,19 @@

+\name{row_dend-HeatmapList-method}

+\alias{row_dend,HeatmapList-method}

+\title{

+Get row dendrograms from a heatmap list

+}

+\description{

+Get row dendrograms from a heatmap list

+}