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

 Type: Package

 Title: Make Complex Heatmaps

 Version: 1.99.5

-Date: 2018-12-30

+Date: 2019-01-31

 Author: Zuguang Gu

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

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

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

-YEAR: 2018

+YEAR: 2019

 COPYRIGHT HOLDER: Zuguang Gu

@@ -197,6 +197,7 @@ export("smartAlign2")

 export("subset_gp")

 export("subset_matrix_by_row")

 export("subset_vector")

+export("test_alter_fun")

 export("unify_mat_list")

 export("upset_right_annotation")

 export("upset_top_annotation")

@@ -2,6 +2,7 @@ CHANGES in VERSION 1.99.5

 * add `UpSet()` and some related functions to make Upset plots

 * fixed bugs of drawing legends

+* add `test_alter_fun()`

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

@@ -615,7 +615,133 @@ guess_alter_fun_is_vectorized = function(alter_fun) {

 # == param

 # -x A strings which encode multiple altertations.

 #

+# == details

+# It recognizes following separators: ``;:,|``.

+#

 default_get_type = function(x) {

 	x = strsplit(x, "\\s*[;:,|]\\s*")[[1]]

 	x[!x %in% c("na", "NA")]

 }

+

+# == title

+# Test alter_fun for oncoPrint()

+#

+# == param

+# -fun The ``alter_fun`` for `oncoPrint`. The value can be a list of functions or a single function. See https://jokergoo.github.io/ComplexHeatmap-reference/book/oncoprint.html#define-the-alter-fun

+# -type A vector of alteration types. It is only used when ``fun`` is a single function.

+# -asp_ratio The aspect ratio (width/height) for the small rectangles.

+#

+# == details

+# This function helps you to have a quick view of how the graphics for each alteration type

+# and combinations look like.

+#

+# == example

+# alter_fun = list(

+# 	mut1 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "red", col = NA)),

+# 	mut2 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "blue", col = NA)),

+# 	mut3 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "yellow", col = NA)),

+# 	mut4 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "purple", col = NA)),

+# 	mut5 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(lwd = 2)),

+# 	mut6 = function(x, y, w, h) grid.points(x, y, pch = 16),

+# 	mut7 = function(x, y, w, h) grid.segments(x - w*0.5, y - h*0.5, x + w*0.5, y + h*0.5, gp = gpar(lwd = 2))

+# )

+# test_alter_fun(alter_fun)

+test_alter_fun = function(fun, type, asp_ratio = 1) {

+	background_fun = NULL

+	if(inherits(fun, "list")) {

+		fun_type = "list"

+		type = names(fun)

+

+		if("background" %in% type) {

+			background_fun = fun$background

+		}

+		type = setdiff(type, "background")

+

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

+			stop_wrap("'type' should be of the names of the function list defined in `fun`.")

+		}

+

+		cat("`alter_fun` is defined as a list of functions.\n")

+		cat("Functions are defined for following alteration types:\n")

+		cat(paste(strwrap(paste(names(fun), collapse = ", "), initial = "  "), collapse = "\n"), "\n")

+		if(!is.null(background_fun)) {

+			cat("Background is also defined.\n")

+		}

+	} else{

+		fun_type = "function"

+		if(length(as.list(formals(fun))) != 5) {

+			stop_wrap("If `alter_fun` is defined as a single function, it needs to have five arguments. Check example at https://jokergoo.github.io/ComplexHeatmap-reference/book/oncoprint.html#define-the-alter-fun.")

+		}

+

+		if(missing(type)) {

+			stop_wrap("You need to provide a vector of alteration types for `type` argument to test.")

+		}

+

+		type = setdiff(type, "background")

+	}

+	

+	tl = lapply(type, function(x) x)

+	names(tl) = type

+	if(length(type) >= 2) {

+		tl2 = as.list(as.data.frame(combn(type, 2), stringsAsFactors = FALSE))

+	} else {

+		tl2 = NULL

+	}

+	if(length(type) >= 3) {

+		tl2 = c(tl2, as.list(as.data.frame(combn(type, 3), stringsAsFactors = FALSE)))

+	}

+

+	if(!is.null(tl2)) {

+		tl2 = tl2[sample(length(tl2), min(length(tl), length(tl2)), prob = sapply(tl2, length))]

+		tl2 = tl2[order(sapply(tl2, length))]

+		names(tl2) = sapply(tl2, paste, collapse = "+")

+	}

+

+	# draw the examples

+	grid_width = asp_ratio*max_text_height("A")*2

+	grid_height = max_text_height("A")*2 + unit(2, "mm")

+	text_width_1 = max_text_width(names(tl))

+	w = text_width_1 + unit(1, "mm") + grid_width

+	if(!is.null(tl2)) {

+		text_width_2 = max_text_width(names(tl2))

+		w = w + unit(5, "mm") + text_width_2 + unit(1, "mm") + grid_width

+	}

+	n = length(tl)

+	h = grid_height*n

+

+	grid.newpage()

+	pushViewport(viewport(width = w, height = h))

+	for(i in 1:n) {

+		grid.text(names(tl)[i], text_width_1, (n - i + 0.5)/n, just = "right")

+		if(is.null(background_fun)) {

+			grid.rect(text_width_1 + unit(1, "mm") + grid_width*0.5, unit((n - i + 0.5)/n, "npc"), grid_width, grid_height - unit(2, "mm"), gp = gpar(fill = "#CCCCCC", col = NA))

+		} else {

+			background_fun(text_width_1 + unit(1, "mm") + grid_width*0.5, unit((n - i + 0.5)/n, "npc"), grid_width, grid_height - unit(2, "mm"))

+		}

+		if(fun_type == "list") {

+			fun[[ tl[[i]] ]](text_width_1 + unit(1, "mm") + grid_width*0.5, unit((n - i + 0.5)/n, "npc"), grid_width, grid_height - unit(2, "mm"))

+		} else {

+			fun(text_width_1 + unit(1, "mm") + grid_width*0.5, unit((n - i + 0.5)/n, "npc"), grid_width, grid_height - unit(2, "mm"), tl[[i]])

+		}

+	}

+	if(!is.null(tl2)) {

+		n2 = length(tl2)

+		for(i in 1:n2) {

+			grid.text(names(tl2)[i], text_width_1 + unit(1, "mm") + grid_width + unit(5, "mm") + text_width_2, (n - i + 0.5)/n, just = "right")

+			if(is.null(background_fun)) {

+				grid.rect(text_width_1 + unit(2, "mm") + unit(5, "mm") + grid_width + text_width_2 + grid_width*0.5, unit((n - i + 0.5)/n, "npc"), grid_width, grid_height - unit(2, "mm"), gp = gpar(fill = "#CCCCCC", col = NA))

+			} else {

+				background_fun(text_width_1 + unit(2, "mm") + unit(5, "mm") + grid_width + text_width_2 + grid_width*0.5, unit((n - i + 0.5)/n, "npc"), grid_width, grid_height - unit(2, "mm"))

+			}

+			if(fun_type == "list") {

+				for(j in tl2[[i]]) {

+					fun[[ j ]](text_width_1 + unit(2, "mm") + unit(5, "mm") + grid_width + text_width_2 + grid_width*0.5, unit((n - i + 0.5)/n, "npc"), grid_width, grid_height - unit(2, "mm"))

+				}

+			} else {

+				fun(text_width_1 + unit(2, "mm") + grid_width + unit(5, "mm") + text_width_2 + grid_width*0.5, unit((n - i + 0.5)/n, "npc"), grid_width, grid_height - unit(2, "mm"), tl2[[i]])

+			}

+		}

+	}

+	popViewport()

+	

+}

@@ -13,6 +13,9 @@ default_get_type(x)

   \item{x}{A strings which encode multiple altertations.}

+}

+\details{

+It recognizes following separators: \code{;:,|}.

 }

 \examples{

 # There is no example

new file mode 100644

@@ -0,0 +1,34 @@

+\name{test_alter_fun}

+\alias{test_alter_fun}

+\title{

+Test alter_fun for oncoPrint()

+}

+\description{

+Test alter_fun for oncoPrint()

+}

+\usage{

+test_alter_fun(fun, type, asp_ratio = 1)

+}

+\arguments{

+

+  \item{fun}{The \code{alter_fun} for \code{\link{oncoPrint}}. The value can be a list of functions or a single function. See \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/oncoprint.html#define-the-alter-fun}}

+  \item{type}{A vector of alteration types. It is only used when \code{fun} is a single function.}

+  \item{asp_ratio}{The aspect ratio (width/height) for the small rectangles.}

+

+}

+\details{

+This function helps you to have a quick view of how the graphics for each alteration type

+and combinations look like.

+}

+\examples{

+alter_fun = list(

+	mut1 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "red", col = NA)),

+	mut2 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "blue", col = NA)),

+	mut3 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "yellow", col = NA)),

+	mut4 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "purple", col = NA)),

+	mut5 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(lwd = 2)),

+	mut6 = function(x, y, w, h) grid.points(x, y, pch = 16),

+	mut7 = function(x, y, w, h) grid.segments(x - w*0.5, y - h*0.5, x + w*0.5, y + h*0.5, gp = gpar(lwd = 2))

+)

+test_alter_fun(alter_fun)

+}