add circos.arrow()

NAMESPACE

@@ -1,4 +1,5 @@
 export('$.CELL_META')
+export('circos.arrow')
 export('circos.axis')
 export('circos.clear')
 export('circos.dendrogram')
@@ -25,7 +26,6 @@ export('circos.nested')
 export('circos.par')
 export('circos.points')
 export('circos.polygon')
-export('circos.raster')
 export('circos.rect')
 export('circos.segments')
 export('circos.text')
@@ -49,6 +49,7 @@ export('get.current.sector.index')
 export('get.current.track.index')
 export('highlight.chromosome')
 export('highlight.sector')
+export('panel.fun')
 export('posTransform.default')
 export('posTransform.text')
 export('print.CELL_META')

NEWS

@@ -2,6 +2,7 @@ Changes in version 0.4.1
 ---------------------------------------------------------------------------
 
 * add `circos.raster()`
+* add `circos.arrow()`
 
 
 Changes in version 0.4.0

R/circos.arrow.R

@@ -0,0 +1,118 @@
+
+# == title
+# Draw arrow which is paralle to the circle
+#
+# == param
+# -x1 start position of the arrow on the x-axis.
+# -x2 end position of the arrow on the x-axis.
+# -y position of the arrow on the y-axis. Note this is the center of the arrow on y-axis.
+# -width width of the arrow body.
+# -sector.index index of the sector.
+# -track.index index of the track.
+# -arrow.head.length length of the arrow head. Note the value should be smaller than the length of the arrow itself (which is ``x2 - x1``).
+# -arrow.head.width width of the arrow head.
+# -arrow.position where is the arrow head on the arrow.
+# -tail the shape of the arrow tail (the opposite side of arrow head).
+# -border border color of the arrow.
+# -col filled color of the arrow.
+# -lty line style of the arrow.
+# -.. pass to `graphics::polygon`.
+#
+# == details
+# Note all position values are measured in the data coordinate (the coordinate in each cell).
+# 
+# If you see points overflow warnings, you can set ``circos.par(points.overflow.warning = FALSE)`` to turn it off.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# circos.initialize(letters[1:4], xlim = c(0, 1))
+# circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+# 	circos.arrow(0, 1, y = 0.5, width = 0.4, arrow.head.length = ux(1, "cm"), 
+# 		col = "red", tail = ifelse(CELL_META$sector.index %in% c("a", "c"), 
+# 			"point", "normal"))
+# }, bg.border = NA, track.height = 0.4)
+#
+# ########## cell cycle ###########
+# cell_cycle = data.frame(phase = c("M", "G1", "S", "G2"),
+# 	                    time = c(1, 11, 8, 4))
+#
+# color = c("#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3")
+# circos.par(start.degree = 90)
+# circos.initialize(cell_cycle$phase, xlim = cbind(rep(0, 4), cell_cycle$time))
+# circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+# 	circos.arrow(CELL_META$xlim[1], CELL_META$xlim[2], 
+# 		arrow.head.width = CELL_META$yrange*0.8, arrow.head.length = ux(1, "cm"),
+# 		col = color[CELL_META$sector.numeric.index])
+# 	circos.text(CELL_META$xcenter, CELL_META$ycenter, CELL_META$sector.index, 
+#		facing = "downward")
+# }, bg.border = NA, track.height = 0.3)
+# circos.clear()
+#
+circos.arrow = function(x1, x2, y = get.cell.meta.data("ycenter", sector.index, track.index), 
+	width = get.cell.meta.data("yrange", sector.index, track.index)/2, 
+	sector.index = get.current.sector.index(), track.index = get.current.track.index(),
+	arrow.head.length = convert_x(5, "mm", sector.index, track.index),
+	arrow.head.width = width*2, arrow.position = c("end", "start"),
+	tail = c("normal", "point"), border = "black", col = "white", lty = par("lty"), ...) {
+
+	arrow.position = match.arg(arrow.position)[1]
+	tail = match.arg(tail)[1]
+
+	sector.index = sector.index
+	track.index = track.index
+
+	if(x2 <= x1) {
+		stop("`x2` should be larger than `x1`.")
+	}
+
+	if(abs(x2 - x1 - arrow.head.length) < 1e-6) {
+		stop("Arrow head is too long that it is even longer than the arrow itself.")
+	}
+
+	if(arrow.position == "end") {
+		arrow.head.coor = rbind(c(x2 - arrow.head.length, y + arrow.head.width/2),
+			                    c(x2, y),
+			                    c(x2 - arrow.head.length, y - arrow.head.width/2))
+		if(tail == "normal") {
+			arrow.body.coor = rbind(c(x2 - arrow.head.length, y - width/2),
+				                    c(x1, y - width/2),
+				                    c(x1, y + width/2),
+				                    c(x2 - arrow.head.length, y + width/2))
+			arrow.body.coor2 = rbind(lines.expand(arrow.body.coor[1:2, 1], arrow.body.coor[1:2, 2], sector.index, track.index),
+				                    lines.expand(arrow.body.coor[3:4, 1], arrow.body.coor[3:4, 2], sector.index, track.index))
+		} else {
+			arrow.body.coor = rbind(c(x2 - arrow.head.length, y - width/2),
+				                    c(x1, y),
+				                    c(x2 - arrow.head.length, y + width/2))
+			arrow.body.coor2 = rbind(lines.expand(arrow.body.coor[1:2, 1], arrow.body.coor[1:2, 2], sector.index, track.index),
+				                    lines.expand(arrow.body.coor[2:3, 1], arrow.body.coor[2:3, 2], sector.index, track.index))
+		}
+
+		coor = rbind(arrow.body.coor2, arrow.head.coor)
+	} else {
+
+		arrow.head.coor = rbind(c(x1 + arrow.head.length, y + arrow.head.width/2),
+			                    c(x1, y),
+			                    c(x1 + arrow.head.length, y - arrow.head.width/2))
+		if(tail == "normal") {
+			arrow.body.coor = rbind(c(x1 + arrow.head.length, y - width/2),
+				                    c(x2, y - width/2),
+				                    c(x2, y + width/2),
+				                    c(x1 + arrow.head.length, y + width/2))
+			arrow.body.coor2 = rbind(lines.expand(arrow.body.coor[1:2, 1], arrow.body.coor[1:2, 2], sector.index, track.index),
+				                    lines.expand(arrow.body.coor[3:4, 1], arrow.body.coor[3:4, 2], sector.index, track.index))
+		} else {
+			arrow.body.coor = rbind(c(x1 + arrow.head.length, y - width/2),
+				                    c(x2, y),
+				                    c(x1 + arrow.head.length, y + width/2))
+			arrow.body.coor2 = rbind(lines.expand(arrow.body.coor[1:2, 1], arrow.body.coor[1:2, 2], sector.index, track.index),
+				                    lines.expand(arrow.body.coor[2:3, 1], arrow.body.coor[2:3, 2], sector.index, track.index))
+		}
+		coor = rbind(arrow.body.coor2, arrow.head.coor)
+	}
+
+	d2 = circlize(coor[, 1], coor[, 2], sector.index, track.index)
+	polygon(polar2Cartesian(d2), border = border, col = col, lty = lty, ...)
+}

man/circos.arrow.rd

@@ -0,0 +1,66 @@
+\name{circos.arrow}
+\alias{circos.arrow}
+\title{
+Draw arrow which is paralle to the circle
+}
+\description{
+Draw arrow which is paralle to the circle
+}
+\usage{
+circos.arrow(x1, x2, y = get.cell.meta.data("ycenter", sector.index, track.index),
+    width = get.cell.meta.data("yrange", sector.index, track.index)/2,
+    sector.index = get.current.sector.index(), track.index = get.current.track.index(),
+    arrow.head.length = convert_x(5, "mm", sector.index, track.index),
+    arrow.head.width = width*2, arrow.position = c("end", "start"),
+    tail = c("normal", "point"), border = "black", col = "white", lty = par("lty"), ...)
+}
+\arguments{
+
+  \item{x1}{start position of the arrow on the x-axis.}
+  \item{x2}{end position of the arrow on the x-axis.}
+  \item{y}{position of the arrow on the y-axis. Note this is the center of the arrow on y-axis.}
+  \item{width}{width of the arrow body.}
+  \item{sector.index}{index of the sector.}
+  \item{track.index}{index of the track.}
+  \item{arrow.head.length}{length of the arrow head. Note the value should be smaller than the length of the arrow itself (which is \code{x2 - x1}).}
+  \item{arrow.head.width}{width of the arrow head.}
+  \item{arrow.position}{where is the arrow head on the arrow.}
+  \item{tail}{the shape of the arrow tail (the opposite side of arrow head).}
+  \item{border}{border color of the arrow.}
+  \item{col}{filled color of the arrow.}
+  \item{lty}{line style of the arrow.}
+  \item{..}{pass to \code{\link[graphics]{polygon}}.}
+
+}
+\details{
+Note all position values are measured in the data coordinate (the coordinate in each cell).
+
+If you see points overflow warnings, you can set \code{circos.par(points.overflow.warning = FALSE)} to turn it off.
+}
+\author{
+Zuguang Gu <z.gu@dkfz.de>
+}
+\examples{
+circos.initialize(letters[1:4], xlim = c(0, 1))
+circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+	circos.arrow(0, 1, y = 0.5, width = 0.4, arrow.head.length = ux(1, "cm"), 
+		col = "red", tail = ifelse(CELL_META$sector.index %in% c("a", "c"), 
+			"point", "normal"))
+}, bg.border = NA, track.height = 0.4)
+
+########## cell cycle ###########
+cell_cycle = data.frame(phase = c("M", "G1", "S", "G2"),
+	                    time = c(1, 11, 8, 4))
+
+color = c("#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3")
+circos.par(start.degree = 90)
+circos.initialize(cell_cycle$phase, xlim = cbind(rep(0, 4), cell_cycle$time))
+circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+	circos.arrow(CELL_META$xlim[1], CELL_META$xlim[2], 
+		arrow.head.width = CELL_META$yrange*0.8, arrow.head.length = ux(1, "cm"),
+		col = color[CELL_META$sector.numeric.index])
+	circos.text(CELL_META$xcenter, CELL_META$ycenter, CELL_META$sector.index, 
+	facing = "downward")
+}, bg.border = NA, track.height = 0.3)
+circos.clear()
+}

man/panel.fun.rd

@@ -0,0 +1,39 @@
+\name{panel.fun}
+\alias{panel.fun}
+\title{
+Add raster images
+}
+\description{
+Add raster images
+}
+\usage{
+panel.fun(x, y)
+}
+\arguments{
+
+  \item{image}{a \code{raster} object, or an object that can be converted by \code{\link[grDevices]{as.raster}}}
+  \item{x}{position of the center of the raster image, measued in the data coordinate in the cell}
+  \item{y}{position of the center of the raster image, measued in the data coordinate in the cell}
+  \item{width}{width of the raster image. When \code{facing} is one of "inside", "outside", "clockwise" and "reverse.clockwise", the image should have absolute size where the value of \code{width} should be specified like \code{20mm}, \code{1cm} or \code{0.5inche}. When \code{facing} is one of \code{bending.inside} and \code{bending.outside}, the value of \code{width} is measured in the data coordinate in the cell.}
+  \item{height}{height of the raster image. Same format as \code{width}. If the value of \code{height} is omit,  default height is calculated by taking the aspect ratio of the original image. But when \code{facing} is one of \code{bending.inside} and \code{bending.outside}, \code{height} is mandatory to set.}
+  \item{facing}{facing of the raster image}
+  \item{niceFacing}{facing of text. Please refer to vignette for different settings}
+  \item{sector.index}{index for the sector}
+  \item{track.index}{index for the track}
+  \item{scaling}{scaling factor to resize the raster image.}
+
+}
+\author{
+Zuguang Gu <z.gu@dkfz.de>
+}
+\examples{
+require(png)
+image = system.file("extdata", "Rlogo.png", package = "circlize")
+image = as.raster(readPNG(image))
+circos.initialize(letters[1:8], xlim = c(0, 1))
+circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+    circos.raster(image, CELL_META$xcenter, CELL_META$ycenter, width = "2cm", 
+        facing = "inside", niceFacing = TRUE)
+})
+circos.clear()
+}