support nicer Chord diagrams

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: circlize
 Type: Package
 Title: Circular Visualization
-Version: 0.4.10
+Version: 0.4.11
 Date: 2020-06-14
 Author: Zuguang Gu
 Maintainer: Zuguang Gu <[email protected]>

NAMESPACE

@@ -7,6 +7,7 @@ export("print.CELL_META")
 export("CELL_META")
 export("add_transparency")
 export("adjacencyList2Matrix")
+export("adjacencyMatrix2List")
 export("calc_gap")
 export("chordDiagram")
 export("chordDiagramFromDataFrame")

NEWS

@@ -1,3 +1,8 @@
+Changes in version 0.4.11
+-----------------------------------------------------------------------
+* `chordDiagram()`: add `link.auto` argument
+* `chordDiagram()`: add `link.target.prop` and `target.prop.height` arguments
+
 Changes in version 0.4.10
 -----------------------------------------------------------------------
 * `highlight.sector()`: fixed a bug when circos.par("clock.wise" = FALSE)

R/circos.arrow.R

@@ -3,23 +3,25 @@
 # 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`.
+# -x1 Start position of the arrow on the x-axis.
+# -x2 End position of the arrow on the x-axis. Note ``x2`` should be larger than ``x1``. The direction
+#     of arrows can be controlled by ``arrow.position`` argument.
+# -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. If you want to the arrow in the reversed direction, set this value to ``"start"``.
+# -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).
+# Note all position values are measured in the data coordinate (the coordinate in each cell). For the values of
+# ``width``, ``arrow.head.Length``, ``arrow.head.width``, they can be set with `mm_y`/`cm_y`/`inches_y` in absolute units.
 # 
 # If you see points overflow warnings, you can set ``circos.par(points.overflow.warning = FALSE)`` to turn it off.
 #
@@ -30,14 +32,30 @@
 # Zuguang Gu <[email protected]>
 #
 # == example
+# op = par(no.readonly = TRUE)
+# par(mfrow = c(1, 2))
 # circos.initialize(letters[1:4], xlim = c(0, 1))
+# col = rand_color(4)
+# tail = c("point", "normal", "point", "normal")
 # 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$sector.index \%in\% c("a", "c"), 
-#           "point", "normal"))
+#     circos.arrow(x1 = 0, x2 = 1, y = 0.5, width = 0.4, 
+#         arrow.head.width = 0.6, arrow.head.length = cm_x(1), 
+#         col = col[CELL_META$sector.numeric.index], 
+#         tail = tail[CELL_META$sector.numeric.index])
 # }, bg.border = NA, track.height = 0.4)
 # circos.clear()
 #
+# circos.initialize(letters[1:4], xlim = c(0, 1))
+# tail = c("point", "normal", "point", "normal")
+# circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+#     circos.arrow(x1 = 0, x2 = 1, y = 0.5, width = 0.4, 
+#         arrow.head.width = 0.6, arrow.head.length = cm_x(1), 
+#         col = col[CELL_META$sector.numeric.index], 
+#         tail = tail[CELL_META$sector.numeric.index],
+#         arrow.position = "start")
+# }, bg.border = NA, track.height = 0.4)
+# par(op)
+#
 # ########## cell cycle ###########
 # cell_cycle = data.frame(phase = factor(c("G1", "S", "G2", "M"), 
 #                                     levels = c("G1", "S", "G2", "M")),
@@ -47,7 +65,7 @@
 # circos.initialize(cell_cycle$phase, xlim = cbind(rep(0, 4), cell_cycle$hour))
 # circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
 #   circos.arrow(CELL_META$xlim[1], CELL_META$xlim[2], 
-#       arrow.head.width = CELL_META$yrange*0.8, arrow.head.length = ux(1, "cm"),
+#       arrow.head.width = CELL_META$yrange*0.8, arrow.head.length = cm_x(1),
 #       col = color[CELL_META$sector.numeric.index])
 #   circos.text(CELL_META$xcenter, CELL_META$ycenter, CELL_META$sector.index, 
 #       facing = "downward")
@@ -57,11 +75,11 @@
 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, 
+	y = get.cell.meta.data("ycenter"), 
+	width = get.cell.meta.data("yrange")/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.length = mm_x(5),
 	arrow.head.width = width*2, 
 	arrow.position = c("end", "start"),
 	tail = c("normal", "point"), 
@@ -73,8 +91,7 @@ circos.arrow = function(
 	arrow.position = match.arg(arrow.position)[1]
 	tail = match.arg(tail)[1]
 
-	sector.index = sector.index
-	track.index = track.index
+	set.current.cell(sector.index, track.index)
 
 	if(x2 <= x1) {
 		stop_wrap("`x2` should be larger than `x1`. Set `arrow.position = 'start'`\nto get reverse clockwise arrows.")

R/circos.heatmap.R

@@ -66,6 +66,9 @@ is.circos.heatmap.cached = function() {
 # -distance.method Distance method, pass to `stats::dist`.
 # -dend.callback A callback function that is applied to the dendrogram in every sector.
 # 
+# == seealso
+# https://jokergoo.github.io/2020/05/21/make-circular-heatmaps/
+#
 circos.heatmap.initialize = function(mat, split = NULL, cluster = TRUE, 
 	clustering.method = "complete", distance.method = "euclidean",
 	dend.callback = function(dend, m, si) reorder(dend, rowMeans(m))) {
@@ -185,6 +188,9 @@ circos.heatmap.validate = function(mat_list) {
 # -show.sector.labels Whether to show sector labels.
 # -... Pass to `circos.track` which draws the heatmap track.
 # 
+# == seealso
+# https://jokergoo.github.io/2020/05/21/make-circular-heatmaps/
+#
 # == example
 # \donttest{
 # set.seed(123)

R/circos.nested.R

@@ -2,16 +2,16 @@
 # Nested zooming with two circular plots
 #
 # == param
-# -f1 a self-defined function for making the first circular plot. The function should have no argument.
-# -f2 a self-defined function for making the second circular plot. The function should have no argument.
-# -correspondance a six-column data frame which contains correspondance between the
+# -f1 A self-defined function for making the first circular plot. The function should have no argument.
+# -f2 A self-defined function for making the second circular plot. The function should have no argument.
+# -correspondance A six-column data frame which contains correspondance between the
 #               coordinates in two circular plots
-# -connection_height the height of the connection track, measured as the percent to the radius of the unit circle.
+# -connection_height The height of the connection track, measured as the percent to the radius of the unit circle.
 #         The value can be specified by `uh` or `convert_height` with absolute units.
-# -connection_col filled color of the connection track. The value can be a vector with same length as number of rows of ``correspondance``
-# -connection_border border color of the connection track.
-# -connection_lty line style of the connection track borders
-# -connection_lwd line width of the connection track borders
+# -connection_col Filled color of the connection track. The value can be a vector with same length as number of rows of ``correspondance``
+# -connection_border Border color of the connection track.
+# -connection_lty Line style of the connection track borders
+# -connection_lwd Line width of the connection track borders
 # -adjust_start_degree If ``circos.par(start.degree = ...)`` is not set in ``f2()``, the start degree for the second
 #       circular plot will be adjusted to make the distance of sectors between the two plots to the minimal.
 #
@@ -38,7 +38,7 @@ circos.nested = function(
 	f1,
 	f2,
 	correspondance,
-	connection_height = convert_height(5, "mm"),
+	connection_height = mm_h(5),
 	connection_col = NA,
 	connection_border = "black",
 	connection_lty = par("lty"),