remove panel.fun.rd

NAMESPACE

@@ -26,6 +26,7 @@ export('circos.nested')
 export('circos.par')
 export('circos.points')
 export('circos.polygon')
+export('circos.raster')
 export('circos.rect')
 export('circos.segments')
 export('circos.text')
@@ -49,7 +50,6 @@ 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')

R/raster.R

@@ -33,7 +33,7 @@
 #         facing = "inside", niceFacing = TRUE)
 # })
 # circos.clear()
-
+#
 # \dontrun{
 # # NOTE: following takes quite a long time to run
 # load(system.file("extdata", "doodle.RData", package = "circlize"))

man/circos.raster.rd

@@ -12,20 +12,20 @@ circos.raster(image, x, y, width, height,
     "downward", "bending.inside", "bending.outside"),
     niceFacing = FALSE, sector.index = get.cell.meta.data("sector.index"),
     track.index = get.cell.meta.data("track.index"),
-    scaling = ifelse(grepl("bend", facing), 0.5, 1))
+    scaling = 1)
 }
 \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 as \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.}
+  \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. The size measured in pixel is calculated according to the size in the final plot. The size can be adjusted by multiplying \code{scaling}.}
+  \item{scaling}{scaling factor to resize the raster image.}
 
 }
 \author{
@@ -37,15 +37,26 @@ 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.raster(image, CELL_META$xcenter, CELL_META$ycenter, width = "2cm", 
+        facing = "inside", niceFacing = TRUE)
 })
+circos.clear()
 
 \dontrun{
-circos.initialize(letters[1:8], xlim = c(0, 1))
+# NOTE: following takes quite a long time to run
+load(system.file("extdata", "doodle.RData", package = "circlize"))
+circos.par("cell.padding" = c(0, 0, 0, 0))
+circos.initialize(letters[1:16], 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")
-})
+    img = img_list[[CELL_META$sector.numeric.index]]
+    circos.raster(img, CELL_META$xcenter, CELL_META$ycenter, width = 1, 
+        height = 1, facing = "bending.inside")
+}, track.height = 0.25, bg.border = NA)
+circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+    img = img_list[[CELL_META$sector.numeric.index + 16]]
+    circos.raster(img, CELL_META$xcenter, CELL_META$ycenter, width = 1, 
+        height = 1, facing = "bending.inside")
+}, track.height = 0.25, bg.border = NA)
+circos.clear()
 }
 }