add circos.raster

DESCRIPTION

@@ -2,25 +2,25 @@ Package: circlize
 Type: Package
 Title: Circular Visualization
 Version: 0.4.0
-Date: 2017-4-14
+Date: 2017-5-29
 Author: Zuguang Gu
 Maintainer: Zuguang Gu <[email protected]>
-Depends: R (>= 2.10.0), graphics
+Depends: R (>= 3.0.0), graphics
 Imports: GlobalOptions (>= 0.0.12), shape, grDevices, utils, stats, 
     colorspace, methods, grid
 Suggests: knitr, dendextend (>= 1.0.1), ComplexHeatmap (>= 1.13.2), gridBase
 VignetteBuilder: knitr
 Description: Circular layout is an efficient way for the visualization of huge 
-    amounts of information. Here the circlize package provides an implementation 
+    amounts of information. Here this package provides an implementation 
     of circular layout generation in R as well as an enhancement of available 
-    software. The flexibility of this package is based on the usage of low-level 
+    software. The flexibility of the package is based on the usage of low-level 
     graphics functions such that self-defined high-level graphics can be easily 
     implemented by users for specific purposes. Together with the seamless 
     connection between the powerful computational and visual environment in R, 
-    circlize gives users more convenience and freedom to design figures for 
-    better understanding complex patterns behind multi-dimensional data.
+    it gives users more convenience and freedom to design figures for 
+    better understanding complex patterns behind multiple dimensional data.
 URL: https://github.com/jokergoo/circlize, http://jokergoo.github.io/circlize_book/book/
 License: GPL (>= 2)
-Packaged: 2017-4-14 00:00:00 UTC; Administrator
+Packaged: 2017-5-29 00:00:00 UTC; Administrator
 Repository: CRAN
-Date/Publication: 2017-4-14 00:00:00
+Date/Publication: 2017-5-29 00:00:00

NAMESPACE

@@ -81,6 +81,7 @@ export(ux)
 export(uy)
 
 S3method(print, CELL_META)
+S3method("$", CELL_META)
 import(graphics)
 importFrom("GlobalOptions", setGlobalOptions)
 importFrom("colorspace", HLS)

R/link.R

@@ -108,7 +108,7 @@ circos.link = function(sector.index1, point1, sector.index2, point2,
 		} else {
 	        if(degreeDiff(theta1, theta21) > degreeDiff(theta1, theta22)) {
 	        	d1 = getQuadraticPoints(theta1, theta21, rou1, rou2, h = h, h.ratio = h.ratio, w = w)
-	        	d2 = getQuadraticPoints(theta1, theta22, rou1, rou2, h = h2, h.ratio = h.ratio, h.ratio = h.ratio, w = w2)
+	        	d2 = getQuadraticPoints(theta1, theta22, rou1, rou2, h = h2, h.ratio = h.ratio, w = w2)
 	        	d1x = getQuadraticPoints(theta1, theta21, rou1, rou2 - arr.length, h = h, h.ratio = h.ratio, w = w)
 	        	d2x = getQuadraticPoints(theta1, theta22, rou1, rou2 - arr.length, h = h2, h.ratio = h.ratio, w = w2)
 	        	dcenter = getQuadraticPoints(theta1, (theta21 + theta22)/2, rou1, rou2, h = (h+h2)/2, h.ratio = h.ratio, w = (w+w2)/2)

R/raster.R

@@ -0,0 +1,161 @@
+
+# if facing  %in% c("bending.inside", "bending.outside"), width and height
+# can be numeric values
+# else facing should be a string like "2cm"
+
+image = system.file("img", "Rlogo.png", package = "png")
+
+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 = 1, 
+		height = 1, facing = "bending.inside")
+})
+circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+	circos.raster(image, CELL_META$xcenter, CELL_META$ycenter, width = runif(1, 0.5, 1), 
+		height = runif(1, 0.5, 1), facing = "bending.inside", niceFacing = TRUE)
+})
+
+circos.raster = function(image, x, y, width, height, 
+	facing = c("inside", "outside", "reverse.clockwise", "clockwise",
+        "downward", "bending", "bending.inside", "bending.outside"),
+    niceFacing = FALSE, sector.index = get.cell.meta.data("sector.index"), 
+    track.index = get.cell.meta.data("track.index"), 
+    resolution = ifelse(grepl("bend", facing), 0.5, 1)) {
+
+	# convert image to Image class (in EBImage package)
+	if(inherits(image, "character")) {
+		image = readImage(image)
+	} else if(!inherits(image, "Image")) {
+		image = as.Image(image)
+	}
+	asp = dim(img)[1]/dim(img)[2]
+
+	facing = match.arg(facing)
+	if(facing %in% c("bending.inside", "bending.outside")) {
+
+		if(niceFacing) {
+			degree = circlize(x, y, sector.index = sector.index, track.index = track.index)[, 1]
+			degree = degree %% 360
+			if(degree > 180 & degree < 360) {
+				if(facing == "bending.inside") {
+					facing = "bending.outside"
+				} else {
+					facing = "bending.inside"
+				}
+			}
+		} 
+
+		pin = par("pin")
+		usr = par("usr")
+
+	    pt_per_inche1 = (usr[2] - usr[1])/pin[1]
+
+	    xplot = get.cell.meta.data("xplot", sector.index = sector.index, track.index = track.index)
+	    cell.xlim = get.cell.meta.data("cell.xlim", sector.index = sector.index, track.index = track.index)
+	    width_in_degree = width/(cell.xlim[2] - cell.xlim[1]) * ((xplot[1] - xplot[2]) %% 360)
+	    yplot = get.cell.meta.data("yplot", sector.index = sector.index, track.index = track.index)
+	    cell.ylim = get.cell.meta.data("cell.ylim", sector.index = sector.index, track.index = track.index)
+	    height_in_native = height/(cell.ylim[2] - cell.ylim[1]) * (yplot[2] - yplot[1])
+
+	    r = yplot[1] + (y - cell.ylim[1])/(cell.ylim[2] - cell.ylim[1]) * (yplot[2] - yplot[1])
+	    width_in_native = pi*as.radian(width_in_degree)*r
+
+	    width_in_px = round(width_in_native/pt_per_inche1*96)
+	    height_in_px = round(height_in_native/pt_per_inche1*96)
+
+		# resize according to the size on the image
+		image = resize(image, w = width_in_px*resolution, h = height_in_px*resolution)
+		image = as.raster(image)
+
+		# make circular rectangles
+		xlim = get.cell.meta.data("xlim", sector.index = sector.index, track.index = track.index)
+		ylim = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)
+
+		nr = nrow(image)
+		nc = ncol(image)
+
+		row_index = rep(1:nr, nc)
+		col_index = rep(1:nc, each = nr)
+
+		if(facing == "bending.inside") {
+			yv = 1 - (row_index - 0.5)/nr
+			xv = (col_index - 0.5)/nc
+		} else {
+			yv = (row_index - 0.5)/nr
+			xv = 1 - (col_index - 0.5)/nc
+		}
+		xv = x - width/2 + xv*width
+		yv = y - height/2 + yv*height
+		l = !grepl("^#FFFFFF", image)
+		circos.rect(xv[l] - width/nc/2, yv[l] - height/nr/2, xv[l] + width/nc/2, yv[l] + height/nr/2,
+			col = image[l], border = image[l], sector.index = sector.index, track.index = track.index)
+
+	} else {
+		if(missing(width) && missing(height)) {
+			stop("at least one of `width` and `height` should be specified")
+		}
+		if(!missing(width)) {
+			width_lt = parse_unit(width)
+			width = width_lt$value
+			width_unit = width_lt$unit
+			width_in_px = switch(width_unit, 
+				mm = width*3.7795275591,
+				cm = width*37.795275591,
+				inche = width*96
+			)
+			width_in_px = round(width_in_px)
+			width_in_native = convert_length(width, width_unit)
+		}
+		if(!missing(height)) {
+			height_lt = parse_unit(height)
+			height = height_lt$value
+			height_unit = height_lt$unit
+			height_in_px = switch(width_unit, 
+				mm = height*3.7795275591,
+				cm = height*37.795275591,
+				inche = height*96
+			)
+			height_in_px = round(height_in_px)
+			height_in_native = convert_length(height, height_unit)
+		}
+
+		if(missig(width)) {
+			width_in_px = round(height_in_px*asp)
+			width_in_native = width_in_native*asp
+		}
+		if(missing(height)) {
+			height_in_px = round(width_in_px/asp)
+			height_in_native = width_in_native*asp
+		}
+
+		df1 = circlize(x, y, sector.index = sector.index, track.index = track.index)
+		df2 = polar2Cartesian(df1)
+		x0 = df2[1, 1]
+		y0 = df2[1, 2]
+
+		# resize accoring to the width and height
+		image = resize(image, w = width_in_px, h = height_in_px)
+
+		theta = df1[1, 1] - 90
+		coor_mat = cbind(c(x0 - width_in_native/2, y0 - height_in_native/2),
+			             c(x0 + width_in_native/2, y0 + height_in_native/2))
+
+		points(corr_mat[, 1], corr_mat[, 2], pch = 16, col = "red")
+
+		# since rasterImage() rotate image at the left bottom corner,
+		# here we move the image to let it rotate at the center of the image
+		rot_mat1 = cbind(c( cos(as.radian(theta)),  sin(as.radian(theta))),
+			             c(-sin(as.radian(theta)),  cos(as.radian(theta))))
+		rot_mat2 = cbind(c( cos(as.radian(-theta)), sin(as.radian(-theta))),
+			             c(-sin(as.radian(-theta)), cos(as.radian(-theta))))
+		coor_mat = coor_mat %*% rot_mat1
+		corr_mat[, 1] = corr_mat[, 1] - width_in_native/2
+		corr_mat[, 2] = corr_mat[, 2] - height_in_native/2
+		corr_mat = corr_mat %*% rot_mat2
+		rasterImage(image, corr_mat[1, 1], corr_mat[1, 2], corr_mat[2, 1], corr_mat[2, 2], angle = theta)
+		points(corr_mat[, 1], corr_mat[, 2], pch = 16, col = "red")
+	}
+}
+
+
+# a function convert unit in data coordinate to absolute unit