@@ -1,12 +1,12 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Making Complex Heatmaps

-Version: 1.7.3

+Version: 1.7.4

 Date: 2015-11-24

 Author: Zuguang Gu

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

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

-Imports: methods, circlize (>= 0.3.1), GetoptLong, colorspace,

+Imports: methods, circlize (>= 0.3.4), GetoptLong, colorspace,

     RColorBrewer, dendextend (>= 1.0.1), GlobalOptions (>= 0.0.6)

 Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust, 

     dendsort, HilbertCurve

@@ -43,8 +43,9 @@ export(anno_barplot)

 exportMethods(row_dend)

 export(row_anno_boxplot)

 export(max_text_width)

-export(decorate_row_title)

+export(anno_link)

 exportMethods(make_layout)

+export(decorate_row_title)

 export(anno_histogram)

 export(plotDataFrame)

 exportMethods(draw_dimnames)

@@ -68,9 +69,10 @@ export(Heatmap)

 exportMethods(draw_annotation_legend)

 exportMethods(column_dend)

 exportMethods(set_component_height)

+export(row_anno_link)

+exportMethods(make_column_cluster)

 export(HeatmapList)

 exportMethods(draw_annotation)

-exportMethods(make_column_cluster)

 export(SingleAnnotation)

 export(row_anno_histogram)

 exportMethods(get_color_mapping_list)

@@ -83,6 +85,7 @@ export(grid.dendrogram)

 export(decorate_title)

 export(decorate_dend)

 export(rowAnnotation)

+export(column_anno_link)

 export(columnAnnotation)

 export(decorate_row_names)

 export(anno_text)

@@ -94,6 +97,7 @@ importFrom("methods", setMethod)

 importFrom("methods", setGeneric)

 importFrom("circlize", colorRamp2)

 importFrom("circlize", rand_color)

+importFrom("circlize", smartAlign)

 importFrom("GetoptLong", qq)

 importFrom("GetoptLong", qqcat)

 importFrom("GetoptLong", qq.options)

@@ -101,6 +105,7 @@ importFrom("colorspace", rainbow_hcl)

 importFrom("colorspace", diverge_hcl)

 importFrom("RColorBrewer", brewer.pal)

 importFrom("dendextend", get_branches_heights)

+importFrom("dendextend", nnodes)

 import(graphics)

 import(stats)

 import(grDevices)

@@ -1,9 +1,19 @@

+CHANEGS in VERSION 1.7.4

+

+* width of the heatmap body are calculated correctly if it is set as a fixed unit

+* there is no dendrogram is nrows in a row-slice is 1

+* add `anno_link()` annotation function

+

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

+

 CHANGES in VERSION 1.7.3

 * `oncoPrint()`: add `barplot_ignore` option to remove alterations

   that are not put on the barplot.

 * `oncoPrint()`: delete extra alter_fun if they are not in the matrix

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

+

 CHANGES in VERSION 1.7.2

 * for `anno_points()`, `anno_barplot()`, `anno_boxplot()`, the name is assigned

@@ -1310,6 +1310,9 @@ setMethod(f = "draw_dend",

     dend = as.dendrogram(hc)

     n = length(labels(dend))

+    if(nnodes(dend) <= 1) {

+        return(invisible(NULL))

+    }

     dend_padding = unit(1, "mm")

     pushViewport(viewport(name = paste(object@name, which, "cluster", k, sep = "_"), ...))

@@ -1555,7 +1558,7 @@ setMethod(f = "component_width",

                 if(!is.unit(object@heatmap_param$width)) {

                     unit(1, "null")

                 } else {

-                    object@heatmap_param$width - sum(component_width(object, c(1:3, 5:7)))

+                    object@heatmap_param$width

                 }

             }

         } else if(k == 5) {

@@ -1699,7 +1702,6 @@ setMethod(f = "draw",

             pushViewport(viewport(layout = layout))

             ht_layout_index = object@layout$layout_index

             ht_graphic_fun_list = object@layout$graphic_fun_list

-            

             for(j in seq_len(nrow(ht_layout_index))) {

                 if(ht_layout_index[j, 1] == 5 && ht_layout_index[j, 2] == 4) {

                     pushViewport(viewport(layout.pos.row = ht_layout_index[j, 1], layout.pos.col = ht_layout_index[j, 2], name = paste(object@name, "heatmap_body_wrap", sep = "_")))

@@ -951,3 +951,161 @@ column_anno_text = function(...) {

 	anno_text(..., which = "column")

 }

+# == title

+# Link annotation with labels

+#

+# == param

+# -at numeric index in the original matrix

+# -labels corresponding labels

+# -which column annotaiton or row annotation

+# -side side of the labels. If it is a column annotation, permitted values are "top" and "bottom";

+#       If it is a row annotation, permitted values are "left" and "right".

+# -lines_gp graphic settings for the segments

+# -labels_gp graphic settings for the labels

+# -padding padding between labels if they are attached to each other

+# -link_width, width of the segments.

+#

+# == details

+# Sometimes there are many rows or columns in the heatmap and we want to mark some of the rows.

+# This annotation function is used to mark these rows and connect labels and corresponding rows

+# with links.

+#

+# == author

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

+anno_link = function(at, labels, which = c("column", "row"), side = ifelse(which == "column", "top", "right"),

+	lines_gp = gpar(), labels_gp = gpar(), padding = 0.25, link_width = NULL) {

+

+	at = at

+	if(!is.numeric(at)) {

+		stop("`at` should be numeric index.")

+	}

+	labels = labels

+	which = match.arg(which)[1]

+	lines_gp = check_gp(lines_gp)

+	labels_gp = check_gp(labels_gp)

+	padding = padding

+

+	od = order(at)

+	at = at[od]

+	labels = labels[od]

+

+	f = switch(which,

+		row = function(index, k = NULL, N = NULL, vp_name = NULL) {

+			n = length(index)

+			l = which(at %in% index)

+			at = at[l]

+			labels = labels[l]

+			int = intersect(index, at)

+			int = structure(seq_along(int), names = int)

+			labels = rev(labels[int[as.character(intersect(at, index))]])

+			

+			pushViewport(viewport(xscale = c(0, 1), yscale = c(0.5, n+0.5)))

+			if(length(labels)) {

+				text_height = convertHeight(grobHeight(textGrob(labels, gp = labels_gp))*(1+padding), "native", valueOnly = TRUE)

+				i2 = rev(which(index %in% at))

+				h1 = n-i2+1 - text_height*0.5

+				h2 = n-i2+1 + text_height*0.5

+				pos = rev(smartAlign(h1, h2, c(0.5, n+0.5)))

+				h = (pos[, 1] + pos[, 2])/2

+

+				if(is.null(link_width)) {

+					if(convertWidth(unit(1, "npc") - max_text_width(labels, gp = labels_gp), "mm", valueOnly = TRUE) < 0) {

+						link_width = unit(0.5, "npc")

+					} else {

+						link_width = unit(1, "npc") - max_text_width(labels, gp = labels_gp)

+					}

+				}

+				n2 = length(labels)

+				if(side == "right") {

+					grid.text(labels, rep(link_width, n2), h, default.units = "native", gp = labels_gp, just = "left")

+					link_width = link_width - unit(1, "mm")

+					grid.segments(unit(rep(0, n2), "npc"), n-i2+1, rep(link_width*(1/3), n2), n-i2+1, default.units = "native", gp = lines_gp)

+					grid.segments(rep(link_width*(1/3), n2), n-i2+1, rep(link_width*(2/3), n2), h, default.units = "native", gp = lines_gp)

+					grid.segments(rep(link_width*(2/3), n2), h, rep(link_width, n2), h, default.units = "native", gp = lines_gp)

+				} else {

+					grid.text(labels, rep(link_width, n2), h, default.units = "native", gp = labels_gp, just = "right")

+					link_width = link_width - unit(1, "mm")

+					grid.segments(unit(rep(1, n2), "npc"), n-i2+1, unit(1, "npc")-rep(link_width*(1/3), n2), n-i2+1, default.units = "native", gp = lines_gp)

+					grid.segments(unit(1, "npc")-rep(link_width*(1/3), n2), n-i2+1, unit(1, "npc")-rep(link_width*(2/3), n2), h, default.units = "native", gp = lines_gp)

+					grid.segments(unit(1, "npc")-rep(link_width*(2/3), n2), h, unit(1, "npc")-rep(link_width, n2), h, default.units = "native", gp = lines_gp)

+				}

+			}

+			upViewport()

+		},

+		column = function(index, vp_name = NULL) {

+			n = length(index)

+			int = intersect(index, at)

+			int = structure(seq_along(int), names = int)

+			labels = rev(labels[int[as.character(intersect(at, index))]])

+			pushViewport(viewport(yscale = c(0, 1), xscale = c(0.5, n+0.5)))

+			text_height = convertWidth(grobHeight(textGrob(labels, gp = labels_gp))*(1+padding), "native", valueOnly = TRUE)

+			i2 = which(index %in% at)

+			h1 = i2 - text_height*0.5

+			h2 = i2 + text_height*0.5

+			pos = smartAlign(h1, h2, c(0.5, n+0.5))

+			h = (pos[, 1] + pos[, 2])/2

+			if(is.null(link_width)) {

+				if(convertHeight(unit(1, "npc") - max_text_width(labels, gp = labels_gp), "mm", valueOnly = TRUE) < 0) {

+					link_width = unit(0.5, "npc")

+				} else {

+					link_width = unit(1, "npc") - max_text_width(labels, gp = labels_gp)

+				}

+			}

+			n2 = length(labels)

+			if(side == "top") {

+				grid.text(labels, h, rep(link_width, n2), default.units = "native", gp = labels_gp, rot = 90, just = "left")

+				link_width = link_width - unit(1, "mm")

+				grid.segments(i2, unit(rep(0, n2), "npc"), i2, rep(link_width*(1/3), n2), default.units = "native", gp = lines_gp)

+				grid.segments(i2, rep(link_width*(1/3), n2), h, rep(link_width*(2/3), n2), default.units = "native", gp = lines_gp)

+				grid.segments(h, rep(link_width*(2/3), n2), h, rep(link_width, n), default.units = "native", gp = lines_gp)

+			} else {

+				grid.text(labels, h, rep(link_width, n2), default.units = "native", gp = labels_gp, rot = 90, just = "right")

+				link_width = link_width - unit(1, "mm")

+				grid.segments(i2, unit(rep(1, n2), "npc"), i2, unit(1, "npc")-rep(link_width*(1/3), n2), default.units = "native", gp = lines_gp)

+				grid.segments(i2, unit(1, "npc")-rep(link_width*(1/3), n2), h, unit(1, "npc")-rep(link_width*(2/3), n2), default.units = "native", gp = lines_gp)

+				grid.segments(h, unit(1, "npc")-rep(link_width*(2/3), n2), h, unit(1, "npc")-rep(link_width, n2), default.units = "native", gp = lines_gp)

+			}

+			upViewport()

+		})

+	attr(f, "which") = which

+	attr(f, "fun") = "anno_link"

+	return(f)

+}

+

+# == title

+# Column annotation which is represented as links

+#

+# == param

+# -... pass to `anno_link`

+#

+# == details

+# A wrapper of `anno_link` with pre-defined ``which`` to ``row``.

+#

+# == value

+# See help page of `anno_link`

+#

+# == author

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

+#

+row_anno_link = function(...) {

+	anno_link(..., which = "row")

+}

+

+# == title

+# Column annotation which is represented as links

+#

+# == param

+# -... pass to `anno_link`

+#

+# == details

+# A wrapper of `anno_link` with pre-defined ``which`` to ``column``.

+#

+# == value

+# See help page of `anno_link`

+#

+# == author

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

+#

+column_anno_link = function(...) {

+	anno_link(..., which = "column")

+}

new file mode 100644

@@ -0,0 +1,36 @@

+\name{anno_link}

+\alias{anno_link}

+\title{

+Link annotation with labels

+}

+\description{

+Link annotation with labels

+}

+\usage{

+anno_link(at, labels, which = c("column", "row"), side = ifelse(which == "column", "top", "right"),

+    lines_gp = gpar(), labels_gp = gpar(), padding = 0.25, link_width = NULL)

+}

+\arguments{

+

+  \item{at}{numeric index in the original matrix}

+  \item{labels}{corresponding labels}

+  \item{which}{column annotaiton or row annotation}

+  \item{side}{side of the labels. If it is a column annotation, permitted values are "top" and "bottom"; If it is a row annotation, permitted values are "left" and "right".}

+  \item{lines_gp}{graphic settings for the segments}

+  \item{labels_gp}{graphic settings for the labels}

+  \item{padding}{padding between labels if they are attached to each other}

+  \item{link_width,}{width of the segments.}

+

+}

+\details{

+Sometimes there are many rows or columns in the heatmap and we want to mark some of the rows.

+This annotation function is used to mark these rows and connect labels and corresponding rows

+with links.

+}

+\author{

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

+}

+\examples{

+# There is no example

+NULL

+}

new file mode 100644

@@ -0,0 +1,29 @@

+\name{column_anno_link}

+\alias{column_anno_link}

+\title{

+Column annotation which is represented as links

+}

+\description{

+Column annotation which is represented as links

+}

+\usage{

+column_anno_link(...)

+}

+\arguments{

+

+  \item{...}{pass to \code{\link{anno_link}}}

+

+}

+\details{

+A wrapper of \code{\link{anno_link}} with pre-defined \code{which} to \code{column}.

+}

+\value{

+See help page of \code{\link{anno_link}}

+}

+\author{

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

+}

+\examples{

+# There is no example

+NULL

+}

new file mode 100644

@@ -0,0 +1,29 @@

+\name{row_anno_link}

+\alias{row_anno_link}

+\title{

+Column annotation which is represented as links

+}

+\description{

+Column annotation which is represented as links

+}

+\usage{

+row_anno_link(...)

+}

+\arguments{

+

+  \item{...}{pass to \code{\link{anno_link}}}

+

+}

+\details{

+A wrapper of \code{\link{anno_link}} with pre-defined \code{which} to \code{row}.

+}

+\value{

+See help page of \code{\link{anno_link}}

+}

+\author{

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

+}

+\examples{

+# There is no example

+NULL

+}

@@ -529,6 +529,23 @@ draw(ht_list, column_title = "reverse axis direction", newpage = FALSE)

 upViewport(2)

 ```

+## Mark some of the rows/columns

+

+From version 1.7.4, a new annotation function `anno_link()` was added which connects labels and subset of the rows

+by links. It is helpful when there are many rows/columns and we want to mark some of the rows (e.g. in a gene expression

+matrix, we want to mark some important genes of interest.)

+

+```{r}

+mat = matrix(rnorm(10000), nr = 1000)

+labels = sample(letters, 20, replace = TRUE)

+Heatmap(mat, show_row_dend = FALSE, show_column_dend = FALSE) + 

+rowAnnotation(link = row_anno_link(at = sample(1000, 20), labels = labels),

+  width = unit(1, "cm") + max_text_width(labels))

+# here unit(1, "cm") is width of segments

+```

+

+There are also two shortcut functions: `row_anno_link()` and `column_anno_link()`.

+

 ## Session info

 ```{r}