@@ -1,8 +1,8 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

-Version: 2.7.1.1012

-Date: 2020-12-14

+Version: 2.7.1.1013

+Date: 2020-12-15

 Author: Zuguang Gu

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

 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

@@ -44,7 +44,10 @@ setMethod(f = "draw_heatmap_body",

     pushViewport(viewport(name = paste(object@name, "heatmap_body", kr, kc, sep = "_"), ...))

     mat = object@matrix[row_order, column_order, drop = FALSE]

-    col_matrix = map_to_colors(object@matrix_color_mapping, mat)

+    oe = try(col_matrix <- map_to_colors(object@matrix_color_mapping, mat), silent = TRUE)

+    if(inherits(oe, "try-error")) {

+        col_matrix = matrix(NA, nrow = nrow(mat), ncol = ncol(mat))

+    }

     nc = ncol(mat)

     nr = nrow(mat)

@@ -8,6 +8,7 @@

 #      value representing whether the alteration is present or absent. 

 #      When the value is a list, the names of the list represent alteration types.

 #      You can use `unify_mat_list` to make all matrix having same row names and column names.

+# -name Name of the oncoPrint. Not necessary to specify.

 # -get_type If different alterations are encoded in the matrix as complex strings, this self-defined function

 #           determines how to extract them. It only works when ``mat`` is a matrix. The default value is `default_get_type`.

 # -alter_fun A single function or a list of functions which defines how to add graphics for different alterations.

@@ -53,7 +54,7 @@

 # == author

 # Zuguang Gu <z.gu@dkfz.de>

 #

-oncoPrint = function(mat, 

+oncoPrint = function(mat, name,

 	get_type = default_get_type,

 	alter_fun, 

 	alter_fun_is_vectorized = NULL,

@@ -182,6 +183,14 @@ oncoPrint = function(mat,

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

 	}

+	if(missing(name)) {

+        name = paste0("matrix_", get_oncoprint_index() + 1)

+        increase_oncoprint_index()

+    } else if(is.null(name)) {

+        name = paste0("matrix_", get_oncoprint_index() + 1)

+        increase_oncoprint_index()

+    }

+

 	oncoprint_row_order = function() {

 		order(rowSums(count_matrix), n_mut, decreasing = TRUE)

 	}

@@ -468,13 +477,17 @@ oncoPrint = function(mat,

 	#####################################################################

 	# the main matrix

-	if(length(col)) {

-		pheudo = c(names(col), rep(NA, nrow(arr)*ncol(arr) - length(col)))

-	} else {

-		pheudo = c("mutation", rep(NA, nrow(arr)*ncol(arr) - 1))

+	if(length(col) == 0) {

 		col = c("mutation" = "black")

 	}

+	pheudo = apply(arr, 1:2, function(x) {

+		if(all(!x)) {

+			return("")

+		} else {

+			paste(all_type[x], collapse = ";")

+		}

+	})

 	dim(pheudo) = dim(arr)[1:2]

 	dimnames(pheudo) = dimnames(arr)[1:2]

@@ -558,7 +571,7 @@ oncoPrint = function(mat,

 		}

 	}

-	ht = Heatmap(pheudo, col = col, 

+	ht = Heatmap(pheudo, name = name, col = col, 

 		rect_gp = gpar(type = "none"), 

 		cluster_rows = cluster_rows, cluster_columns = cluster_columns, 

 		row_order = row_order, column_order = column_order,

@@ -54,8 +54,8 @@ heatmap = function(x,

     margins = c(5, 5), 

     ColSideColors, 

     RowSideColors,

-    cexRow = 0.2 + 1/log10(nr), 

-    cexCol = 0.2 + 1/log10(nc),

+    cexRow = 0.6, 

+    cexCol = 0.6,

     labRow = NULL, 

     labCol = NULL, 

     main = NULL,

@@ -368,7 +368,7 @@ heatmap.2 = function(x,

     # data scaling

     scale = c("none","row", "column"),

-    na.rm=TRUE,

+    na.rm = TRUE,

     # image plot

     revC = identical(Colv, "Rowv"),

@@ -376,36 +376,36 @@ heatmap.2 = function(x,

     # mapping data to colors

     breaks,

-    symbreaks=any(x < 0, na.rm=TRUE) || scale!="none",

+    symbreaks = any(x < 0, na.rm = TRUE) || scale != "none",

     # colors

-    col="heat.colors",

+    col = "heat.colors",

     # block sepration

     colsep,

     rowsep,

-    sepcolor="white",

-    sepwidth=c(0.05,0.05),

+    sepcolor = "white",

+    sepwidth = c(0.05, 0.05),

     # cell labeling

     cellnote,

-    notecex=1.0,

-    notecol="cyan",

-    na.color=par("bg"),

+    notecex = 0.6,

+    notecol = "cyan",

+    na.color = par("bg"),

     # level trace

-    trace=c("column","row","both","none"),

-    tracecol="cyan",

-    hline=median(breaks),

-    vline=median(breaks),

-    linecol=tracecol,

+    trace = c("column", "row", "both", "none"),

+    tracecol = "cyan",

+    hline = median(breaks),

+    vline = median(breaks),

+    linecol = tracecol,

     # Row/Column Labeling

     margins = c(5, 5),

     ColSideColors,

     RowSideColors,

-    cexRow = 0.2 + 1/log10(nr),

-    cexCol = 0.2 + 1/log10(nc),

+    cexRow = 0.6,

+    cexCol = 0.6,

     labRow = NULL,

     labCol = NULL,

     srtRow = NULL,

@@ -420,16 +420,16 @@ heatmap.2 = function(x,

     # color key + density info

     key = TRUE,

     keysize = 1.5,

-    density.info=c("histogram","density","none"),

-    denscol=tracecol,

-    symkey = any(x < 0, na.rm=TRUE) || symbreaks,

+    density.info = c("histogram", "density", "none"),

+    denscol = tracecol,

+    symkey = any(x < 0, na.rm = TRUE) || symbreaks,

     densadj = 0.25,

     key.title = NULL,

     key.xlab = NULL,

     key.ylab = NULL,

     key.xtickfun = NULL,

     key.ytickfun = NULL,

-    key.par=list(),

+    key.par = list(),

     # plot labels

     main = NULL,

@@ -442,7 +442,7 @@ heatmap.2 = function(x,

     lwid = NULL,

     # extras

-    extrafun=NULL,

+    extrafun = NULL,

     ...

     ) {

@@ -458,6 +458,10 @@ heatmap.2 = function(x,

     ht_param = list()

+    if(identical(Rowv, FALSE) && identical(symm, TRUE)) {

+        Colv = FALSE

+    }

+

     # Rowv can be 1. NA, 2. a dendrogram object, 3. a vector, 4. a logical value, 5. NULL

     if(identical(Rowv, NA) || identical(Rowv, NULL) || identical(Rowv, FALSE)) {

         ht_param$cluster_rows = FALSE

@@ -571,7 +575,7 @@ heatmap.2 = function(x,

     n_col = ncol

-    if(identical(scale, "row") || identical(scale, "column")) {

+    if(exists("extreme")) {

         lim = max(abs(mat), na.rm = TRUE)

         ht_param$col = colorRamp2(seq(-lim, lim, length = n_col), col)

     } else {

@@ -604,7 +608,7 @@ heatmap.2 = function(x,

             show_legend = FALSE, show_annotation_name = FALSE)

     }

-    if(identical(ht_param$cluster_rows, FALSE)) {

+    if(identical(ht_param$cluster_rows, FALSE) || dendrogram %in% c("none", "column")) {

         if(is.null(ht_param$left_annotation)) {

             ht_param$left_annotation = rowAnnotation(foo1 = anno_empty(width = unit(4, "cm"), border = FALSE))

         } else {

@@ -612,7 +616,7 @@ heatmap.2 = function(x,

         }

     }

-    if(identical(ht_param$cluster_columns, FALSE)) {

+    if(identical(ht_param$cluster_columns, FALSE) || dendrogram %in% c("none", "row")) {

         if(is.null(ht_param$top_annotation)) {

             ht_param$top_annotation = HeatmapAnnotation(foo2 = anno_empty(height = unit(3, "cm"), border = FALSE))

         } else {

@@ -643,9 +647,13 @@ heatmap.2 = function(x,

     if(!is.null(srtRow)) {

         ht_param$row_names_rot = srtRow

+    } else {

+        ht_param$row_names_rot = 0

     }

     if(!is.null(srtCol)) {

         ht_param$column_names_rot = srtCol

+    } else {

+        ht_param$column_names_rot = 90

     }

     if(!is.null(main)) {

@@ -656,7 +664,7 @@ heatmap.2 = function(x,

             ht_param$bottom_annotation = HeatmapAnnotation(xlab = anno_block(labels = xlab, gp = gpar(col = NA)))

         } else {

             ht_param$bottom_annotation = HeatmapAnnotation(

-                colnames = anno_text(ht_param$column_labels, gp = ht_param$column_names_gp),

+                colnames = anno_text(ht_param$column_labels, gp = ht_param$column_names_gp, rot = ht_param$column_names_rot),

                 xlab = anno_block(labels = xlab, gp = gpar(col = NA))

             )

             ht_param$show_column_names = FALSE

@@ -667,7 +675,7 @@ heatmap.2 = function(x,

             ht_param$right_annotation = rowAnnotation(ylab = anno_block(labels = ylab, gp = gpar(col = NA)))

         } else {

             ht_param$right_annotation = rowAnnotation(

-                rownames = anno_text(ht_param$row_labels, gp = ht_param$row_names_gp),

+                rownames = anno_text(ht_param$row_labels, gp = ht_param$row_names_gp, rot = ht_param$row_names_rot),

                 ylab = anno_block(labels = ylab, gp = gpar(col = NA))

             )

             ht_param$show_row_names = FALSE

@@ -717,7 +725,7 @@ heatmap.2 = function(x,

             }

         }

     }

-    if(!is.null(ht_param$layer_fun)) {

+    if(!is.null(ht_param$layer_fun) && trace %in% c("row", "column")) {

         fun1 = ht_param$layer_fun

         fun2 = layer_fun

         fun3 = function(j, i, x, y, w, h, fill) {

@@ -725,9 +733,10 @@ heatmap.2 = function(x,

             fun2(j, i, x, y, w, h, fill)

         }

         layer_fun = fun3

+        ht_param$layer_fun = layer_fun

+    } else if(is.null(ht_param$layer_fun) && trace %in% c("row", "column")) {

+        ht_param$layer_fun = layer_fun

     }

-    ht_param$layer_fun = layer_fun

-

     random_str = paste(sample(c(letters, LETTERS, 0:9), 8), collapse = "")

     ht_param$name = paste0("heatmap.2_", random_str)

@@ -24,6 +24,14 @@ increase_heatmap_index = function() {

 	INDEX_ENV$I_HEATMAP = INDEX_ENV$I_HEATMAP + 1

 }

+get_oncoprint_index = function() {

+    INDEX_ENV$I_ONCOPRINT

+}

+

+increase_oncoprint_index = function() {

+    INDEX_ENV$I_ONCOPRINT = INDEX_ENV$I_ONCOPRINT + 1

+}

+

 get_annotation_index = function() {

 	INDEX_ENV$I_ANNOTATION

 }

@@ -15,4 +15,5 @@ method and the \code{\%v\%v} method so that above three classes can be appended

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -22,4 +22,5 @@ See \code{\link{AnnotationFunction}} constructor for details.

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -40,4 +40,5 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok

 \examples{

 # There is no example

 NULL

+

 }

@@ -22,4 +22,5 @@ Internally used.

 \examples{

 # There is no example

 NULL

+

 }

@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -212,4 +212,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -25,4 +25,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -84,4 +84,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -40,4 +40,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{adjust_heatmap_list-HeatmapList-method}

 \alias{adjust_heatmap_list,HeatmapList-method}

+\alias{adjust_heatmap_list}

 \title{

 Adjust Heatmap List

 }

@@ -23,8 +24,8 @@ This function is only for internal use.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{adjust_heatmap_list}

 \examples{

 # There is no example

 NULL

+

 }

@@ -20,4 +20,5 @@ This function is the same as \code{\link{anno_zoom}}. It links subsets of rows o

 \examples{

 # There is no example

 NULL

+

 }

@@ -35,4 +35,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{annotation_legend_size-HeatmapList-method}

 \alias{annotation_legend_size,HeatmapList-method}

+\alias{annotation_legend_size}

 \title{

 Size of the Annotation Legends

 }

@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{annotation_legend_size}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{attach_annotation-Heatmap-method}

 \alias{attach_annotation,Heatmap-method}

+\alias{attach_annotation}

 \title{

 Attach heatmap annotations to the heatmap

 }

@@ -28,4 +29,3 @@ ha2 = HeatmapAnnotation(bar = letters[1:10])

 ht = attach_annotation(ht, ha2)

 ht

 }

-\alias{attach_annotation}

@@ -23,4 +23,5 @@ A \code{\link[GenomicRanges:GRanges-class]{GRanges}} object of the genomic bins.

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{color_mapping_legend-ColorMapping-method}

 \alias{color_mapping_legend,ColorMapping-method}

+\alias{color_mapping_legend}

 \title{

 Draw Legend Based on Color Mapping

 }

@@ -69,8 +70,8 @@ A \code{\link{Legends-class}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{color_mapping_legend}

 \examples{

 # There is no example

 NULL

+

 }

@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -20,4 +20,5 @@ If there is no complement set, it returns zero.

 \examples{

 # There is no example

 NULL

+

 }

@@ -31,4 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -24,4 +24,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ The environment is at \code{object@var_env}.

 \examples{

 # There is no example

 NULL

+

 }

@@ -21,4 +21,5 @@ it calls \code{\link{copy_all,AnnotationFunction-method}} to hard copy the varia

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -20,4 +20,5 @@ It recognizes following separators: \code{;:,|}.

 \examples{

 # There is no example

 NULL

+

 }

@@ -17,4 +17,5 @@ dend_heights(x)

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ A \code{\link{grob}} object which is contructed by \code{\link[grid:grid.segment

 \examples{

 # There is no example

 NULL

+

 }

@@ -17,4 +17,5 @@ Dimension of the Heatmap

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ which is generally for testing purpose.

 \examples{

 # There is no example

 NULL

+

 }

@@ -33,4 +33,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -202,4 +202,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_annotation-Heatmap-method}

 \alias{draw_annotation,Heatmap-method}

+\alias{draw_annotation}

 \title{

 Draw Heatmap Annotations on the Heatmap

 }

@@ -30,8 +31,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_annotation}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_annotation_legend-HeatmapList-method}

 \alias{draw_annotation_legend,HeatmapList-method}

+\alias{draw_annotation_legend}

 \title{

 Draw legends for All Annotations

 }

@@ -31,8 +32,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_annotation_legend}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_dend-Heatmap-method}

 \alias{draw_dend,Heatmap-method}

+\alias{draw_dend}

 \title{

 Draw Heatmap Dendrograms

 }

@@ -33,8 +34,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_dend}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_dimnames-Heatmap-method}

 \alias{draw_dimnames,Heatmap-method}

+\alias{draw_dimnames}

 \title{

 Draw row names or column names

 }

@@ -29,8 +30,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_dimnames}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_heatmap_body-Heatmap-method}

 \alias{draw_heatmap_body,Heatmap-method}

+\alias{draw_heatmap_body}

 \title{

 Draw Heatmap Body

 }

@@ -28,8 +29,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_heatmap_body}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_heatmap_legend-HeatmapList-method}

 \alias{draw_heatmap_legend,HeatmapList-method}

+\alias{draw_heatmap_legend}

 \title{

 Draw legends for All Heatmaps

 }

@@ -32,8 +33,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_heatmap_legend}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_heatmap_list-HeatmapList-method}

 \alias{draw_heatmap_list,HeatmapList-method}

+\alias{draw_heatmap_list}

 \title{

 Draw the List of Heatmaps

 }

@@ -25,8 +26,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_heatmap_list}

 \examples{

 # There is no example

 NULL

+

 }

@@ -32,4 +32,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{get_color_mapping_list-HeatmapAnnotation-method}

 \alias{get_color_mapping_list,HeatmapAnnotation-method}

+\alias{get_color_mapping_list}

 \title{

 Get a List of ColorMapping objects

 }

@@ -25,8 +26,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{get_color_mapping_list}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{get_legend_param_list-HeatmapAnnotation-method}

 \alias{get_legend_param_list,HeatmapAnnotation-method}

+\alias{get_legend_param_list}

 \title{

 Get a List of Annotation Legend Parameters

 }

@@ -25,8 +26,8 @@ A list.

 \author{

 Zuguang Gu <z.gu@dkfz.de>