@@ -2,7 +2,7 @@ Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

 Version: 2.1.0

-Date: 2019-05-03

+Date: 2019-07-02

 Author: Zuguang Gu

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

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

@@ -2,6 +2,7 @@ CHANGES in VERSION 2.1.0

 * check the length of the clustering objects and the matrix rows/columns

 * `anno_oncoprint_barplot()`: add `ylim` argumnet

+* `anno_mark()`: add `labels_rot` argument

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

@@ -2704,6 +2704,7 @@ row_anno_text = function(...) {

 # -lines_gp Please use ``link_gp`` instead.

 # -link_gp Graphic settings for the segments.

 # -labels_gp Graphic settings for the labels.

+# -labels_rot Rotations of labels, scalar.

 # -padding Padding between neighbouring labels in the plot.

 # -link_width Width of the segments.

 # -link_height Similar as ``link_width``, used for column annotation.

@@ -2732,7 +2733,8 @@ row_anno_text = function(...) {

 # Heatmap(m) + rowAnnotation(mark = anno)

 anno_mark = function(at, labels, which = c("column", "row"), 

 	side = ifelse(which == "column", "top", "right"),

-	lines_gp = gpar(), labels_gp = gpar(), padding = 0.5, 

+	lines_gp = gpar(), labels_gp = gpar(), 

+	labels_rot = ifelse(which == "column", 90, 0), padding = 0.5, 

 	link_width = unit(5, "mm"), link_height = link_width,

 	link_gp = lines_gp, 

 	extend = unit(0, "mm")) {

@@ -2759,9 +2761,9 @@ anno_mark = function(at, labels, which = c("column", "row"),

 	if(which == "row") {

 		height = unit(1, "npc")

-		width = link_width + max_text_width(labels, gp = labels_gp)

+		width = link_width + max_text_width(labels, gp = labels_gp, rot = labels_rot)

 	} else {

-		height = link_width + max_text_width(labels, gp = labels_gp)

+		height = link_width + max_text_height(labels, gp = labels_gp, rot = labels_rot)

 		width = unit(1, "npc")

 	}

@@ -2801,13 +2803,13 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		n2 = length(labels)

 		if(side == "right") {

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

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

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

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

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

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

 		} else {

-			grid.text(labels, unit(1, "npc")-rep(link_width, n2), h, default.units = "native", gp = labels_gp, just = "right")

+			grid.text(labels, unit(1, "npc")-rep(link_width, n2), h, default.units = "native", gp = labels_gp, rot = labels_rot, just = "right")

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

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

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

@@ -2847,13 +2849,13 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		n2 = length(labels)

 		if(side == "top") {

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

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

 			link_height = link_height - unit(1, "mm")

 			grid.segments(pos, unit(rep(0, n2), "npc"), pos, rep(link_height*(1/3), n2), default.units = "native", gp = link_gp)

 			grid.segments(pos, rep(link_height*(1/3), n2), h, rep(link_height*(2/3), n2), default.units = "native", gp = link_gp)

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

 		} else {

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

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

 			link_height = link_height - unit(1, "mm")

 			grid.segments(pos, unit(rep(1, n2), "npc"), pos, unit(1, "npc")-rep(link_height*(1/3), n2), default.units = "native", gp = link_gp)

 			grid.segments(pos, unit(1, "npc")-rep(link_height*(1/3), n2), h, unit(1, "npc")-rep(link_height*(2/3), n2), default.units = "native", gp = link_gp)

@@ -2875,7 +2877,7 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		width = width,

 		height = height,

 		n = -1,

-		var_import = list(at, labels2index, at2labels, link_gp, labels_gp, padding, .pos, .scale,

+		var_import = list(at, labels2index, at2labels, link_gp, labels_gp, labels_rot, padding, .pos, .scale,

 			side, link_width, link_height, extend),

 		show_name = FALSE

 	)

@@ -341,6 +341,7 @@ list_components = function() {

 # == param

 # -text A vector of text.

 # -gp Graphic parameters for text.

+# -rot Rotation of the text, scalar.

 #

 # == details

 # It simply calculates maximum width of a list of `grid::textGrob` objects.

@@ -360,14 +361,14 @@ list_components = function() {

 # x = c("a", "bb", "ccc")

 # max_text_width(x, gp = gpar(fontsize = 10))

 #

-max_text_width = function(text, gp = gpar()) {

+max_text_width = function(text, gp = gpar(), rot = 0) {

     if(is.null(text)) {

         return(unit(0, "mm"))

     }

     n = length(text)

     gp = recycle_gp(gp, n)

-    u = max(do.call("unit.c", lapply(seq_len(n), function(i) grobWidth(textGrob(text[i], gp = subset_gp(gp, i))))))

+    u = max(do.call("unit.c", lapply(seq_len(n), function(i) grobWidth(textGrob(text[i], gp = subset_gp(gp, i), rot = rot)))))

     convertWidth(u, "mm")

 }

@@ -377,6 +378,7 @@ max_text_width = function(text, gp = gpar()) {

 # == param

 # -text A vector of text.

 # -gp Graphic parameters for text.

+# -rot Rotation of the text, scalar.

 #

 # == details

 # It simply calculates maximum height of a list of `grid::textGrob` objects.

@@ -396,14 +398,14 @@ max_text_width = function(text, gp = gpar()) {

 # x = c("a", "b\nb", "c\nc\nc")

 # max_text_height(x, gp = gpar(fontsize = 10))

 #

-max_text_height = function(text, gp = gpar()) {

+max_text_height = function(text, gp = gpar(), rot = 0) {

     if(is.null(text)) {

         return(unit(0, "mm"))

     }

     n = length(text)

     gp = recycle_gp(gp, n)

-    u = max(do.call("unit.c", lapply(seq_len(n), function(i) grobHeight(textGrob(text[i], gp = subset_gp(gp, i))))))

+    u = max(do.call("unit.c", lapply(seq_len(n), function(i) grobHeight(textGrob(text[i], gp = subset_gp(gp, i), rot = rot)))))

     convertHeight(u, "mm")

 }

new file mode 100644

@@ -0,0 +1,91 @@

+

+

+logo = readLines(textConnection("

+oooooo                  oooooo  oo          oo  oo

+oooooo                  oooooo  oo          oo  oo

+oo      oooooo  oo  oo  oo  oo  oo  oooooo  oooooo

+oo      oooooo  oooooo  oo  oo  oo  oooooo  oooooo

+oo      oo  oo  oooooo  oooo    oo  oo  oo    oo

+oo      oo  oo  oooooo  oooo    oo  oo  oo    oo

+oooooo  oooooo  oo  oo  oo      oo  oooo    oo  oo

+oooooo  oooooo  oo  oo  oo      oo  oooo    oo  oo

+

+oo  oo                    oo                    oooooo

+oo  oo                    oo                    oooooo

+oo  oo  oooooo    oooo  oooooo  oo  oo  oooooo  oo  oo

+oo  oo  oooooo    oooo  oooooo  oooooo  oooooo  oo  oo

+oooooo  oo  oo  oo  oo    oo    oooooo  oo  oo  oooo

+oooooo  oo  oo  oo  oo    oo    oooooo  oo  oo  oooo

+oo  oo  oooo    oooooo    oo    oo  oo  oooo    oo

+oo  oo  oooo    oooooo    oo    oo  oo  oooo    oo

+"))

+

+logo = strsplit(logo, "")

+

+mat1 = matrix(0, nrow = 8, ncol = max(sapply(logo[2:9], length)))

+for(i in 2:9) {

+	mat1[i - 1, which(!grepl("^\\s*$", logo[[i]]))] = 1

+}

+mat1 = cbind(matrix(0, nrow = nrow(mat1), ncol = 2), mat1)

+

+mat2 = matrix(0, nrow = 8, ncol = max(sapply(logo[11:18], length)))

+for(i in 11:18) {

+	mat2[i - 10, which(!grepl("^\\s*$", logo[[i]]))] = 1

+}

+

+mat = cbind(mat1, matrix(0, nrow = nrow(mat1), ncol = 4), mat2)

+

+if(ncol(mat1) > ncol(mat2)) {

+	mat2 = cbind(mat2, matrix(0, nrow = nrow(mat2), ncol = ncol(mat1) - ncol(mat2)))

+} else {

+	mat1 = cbind(mat1, matrix(0, nrow = nrow(mat1), ncol = ncol(mat2) - ncol(mat1)))

+}

+

+mat = rbind(mat1, matrix(0, nrow = 2, ncol = ncol(mat1)), mat2)

+

+mat = rbind(matrix(0, nrow = 30, ncol = ncol(mat1)),

+	        mat,

+	        matrix(0, nrow = 30, ncol = ncol(mat1)))

+

+mat = cbind(matrix(0, nrow = nrow(mat), ncol = 10),

+	        mat,

+	        matrix(0, nrow = nrow(mat), ncol = 10))

+

+mat[nrow(mat) - 27, 9:(ncol(mat) - 8)] = 1

+mat[nrow(mat) - 26, 9:(ncol(mat) - 8)] = 1

+mat[28, 9:(ncol(mat) - 8)] = 1

+mat[27, 9:(ncol(mat) - 8)] = 1

+

+

+

+library(ComplexHeatmap)

+library(circlize)

+col_fun = function(x) {

+	n = length(x)

+	col = ifelse(x == 1, add_transparency("#4DAF4A", runif(n, min = 0, max = 0.3)),

+		                 rand_color(n, luminosity = "light", transparency = 0.8))

+}

+attr(col_fun, "breaks") = c(0, 1)

+ht = Heatmap(mat, name = "foo", rect_gp = gpar(col = "white", lwd = 0.5), cluster_rows = FALSE, cluster_columns = FALSE,

+	col = col_fun, show_heatmap_legend = FALSE)

+g = grid.grabExpr(draw(ht, padding = unit(c(0, 0, 0, 0), "mm")))

+

+grid.newpage()

+pushViewport(viewport(xscale = c(0, 2), yscale = c(0, 2), width = unit(0.9, "snpc"), height = unit(0.9, "snpc")))

+grid.polygon(cos(0:5 * pi/3 + pi/6)*1 + 1,

+     sin(0:5 * pi/3 + pi/6)*1 + 1, default.units = "native",

+     gp = gpar(col = "#4DAF4A", lwd = 6))

+height = 1

+pushViewport(viewport(x = 0.5, y = 0.5, height = height, width = height*ncol(mat)/nrow(mat)))

+grid.draw(g)

+popViewport()

+grid.polygon(cos(0:5 * pi/3 + pi/6)*1 + 1,

+     sin(0:5 * pi/3 + pi/6)*1 + 1, default.units = "native",

+     gp = gpar(col = "#4DAF4A", lwd = 8))

+popViewport()

+

+library(gridgeometry)

+A = g

+B = polygonGrid(cos(0:5 * pi/3 + pi/6)*1 + 1,

+     sin(0:5 * pi/3 + pi/6)*1 + 1, default.units = "native",

+     gp = gpar(col = "#4DAF4A", lwd = 8))

@@ -9,7 +9,8 @@ Link annotation with labels

 \usage{

 anno_mark(at, labels, which = c("column", "row"),

     side = ifelse(which == "column", "top", "right"),

-    lines_gp = gpar(), labels_gp = gpar(), padding = 0.5,

+    lines_gp = gpar(), labels_gp = gpar(),

+    labels_rot = ifelse(which == "column", 90, 0), padding = 0.5,

     link_width = unit(5, "mm"), link_height = link_width,

     link_gp = lines_gp,

     extend = unit(0, "mm"))

@@ -23,6 +24,7 @@ anno_mark(at, labels, which = c("column", "row"),

   \item{lines_gp}{Please use \code{link_gp} instead.}

   \item{link_gp}{Graphic settings for the segments.}

   \item{labels_gp}{Graphic settings for the labels.}

+  \item{labels_rot}{Rotations of labels, scalar.}

   \item{padding}{Padding between neighbouring labels in the plot.}

   \item{link_width}{Width of the segments.}

   \item{link_height}{Similar as \code{link_width}, used for column annotation.}

@@ -7,12 +7,13 @@ Maximum Height of Text

 Maximum Height of Text

 }

 \usage{

-max_text_height(text, gp = gpar())

+max_text_height(text, gp = gpar(), rot = 0)

 }

 \arguments{

   \item{text}{A vector of text.}

   \item{gp}{Graphic parameters for text.}

+  \item{rot}{Rotation of the text, scalar.}

 }

 \details{

@@ -7,12 +7,13 @@ Maximum Width of Text

 Maximum Width of Text

 }

 \usage{

-max_text_width(text, gp = gpar())

+max_text_width(text, gp = gpar(), rot = 0)

 }

 \arguments{

   \item{text}{A vector of text.}

   \item{gp}{Graphic parameters for text.}

+  \item{rot}{Rotation of the text, scalar.}

 }

 \details{

@@ -293,8 +293,11 @@ draw(anno, test = "heatmap, colors")

 anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")

 draw(anno, index = 1:100, test = "anno_mark")

+anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], labels_rot = 30, which = "row")

+draw(anno, index = 1:100, test = "anno_mark")

+

 m = matrix(1:1000, byrow = TRUE, nr = 100)

-anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")

+anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row", labels_rot = 30)

 Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)

 Heatmap(m) + rowAnnotation(mark = anno)