add arrange_links_evenly()

NAMESPACE

@@ -8,6 +8,7 @@ export("CELL_META")
 export("add_transparency")
 export("adjacencyList2Matrix")
 export("adjacencyMatrix2List")
+export("arrange_links_evenly")
 export("calc_gap")
 export("chordDiagram")
 export("chordDiagramFromDataFrame")

NEWS

@@ -10,6 +10,7 @@ Changes in version 0.4.12
 * `circos.genomicLabels()`: replace `side` argument with `labels.side`.
 * `circos.points()`, `circos.lines()`, `circos.text()` allow argument `x` to be
   a two-column matrix.
+* add `arrange_links_evenly()` function.
 
 Changes in version 0.4.11
 -----------------------------------------------------------------------

R/chordDiagram.R

@@ -754,6 +754,7 @@ chordDiagramFromMatrix = function(
 # -group It contains the group labels and the sector names are used as the names in the vector.
 # -big.gap Gaps between the sectors in the first column of ``df`` and sectors in the second column in ``df``.
 # -small.gap Small gap between sectors.
+# -plot Internally used.
 # -... pass to `circos.link`
 #
 # == details
@@ -804,6 +805,7 @@ chordDiagramFromDataFrame = function(
 	group = NULL,
 	big.gap = 10,
 	small.gap = 1,
+	plot = TRUE,
 	...) {
 
 	if(!is.null(link.rank)) {
@@ -1219,6 +1221,8 @@ chordDiagramFromDataFrame = function(
 		xsum = pmax(x1_sum, x2_sum)
 	}
 
+	if(!plot) return(df)
+
 	o.cell.padding = circos.par("cell.padding")
 	circos.par(cell.padding = c(0, 0, 0, 0))
     o.start.degree = circos.par("start.degree")

R/link.R

@@ -650,3 +650,70 @@ line_degree = function(x0, y0, x1, y1) {
 	if(x0 > x1 && y0 < y1) alpha = (alpha + 180) %% 360
 	return(alpha)
 }
+
+
+# == title
+# Arrange links evenly on each sector
+#
+# == param
+# -df A data frame with two columns. The values should only contain sector names.
+#
+# == details
+# This function only deals with single-line links.
+#
+# == value
+# A data frame with four columns of the sectors and the positions of the links.
+#
+# == example
+# sectors = letters[1:20]
+# df = data.frame(from = sample(sectors, 40, replace = TRUE),
+#                 to   = sample(sectors, 40, replace = TRUE))
+# df = unique(df)
+# df = df[df$from != df$to, ]
+#
+# circos.initialize(sectors, xlim = c(0, 1))
+# circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+#     circos.text(CELL_META$xcenter, CELL_META$ycenter, CELL_META$sector.index)
+# })
+#
+# df2 = arrange_links_evenly(df)
+#
+# for(i in seq_len(nrow(df2))) {
+#     s1 = df$from[i]
+#     s2 = df$to[i]
+#     circos.link(df2[i, "sector1"], df2[i, "pos1"], 
+#                 df2[i, "sector2"], df2[i, "pos2"],
+#                 directional = 1)
+# }
+#
+arrange_links_evenly = function(df) {
+
+    if(!is.circos.initialized()) {
+        stop_wrap("Circular layout needs to be initialized.")
+    }
+
+    df[, 1] = factor(df[, 1], levels = get.all.sector.index())
+    df[, 2] = factor(df[, 2], levels = get.all.sector.index())
+
+    if(any(is.na(df[, 1])) || any(is.na(df[, 2]))) {
+    	stop_wrap("The two columns in `df` should only contain sector names.")
+    }
+
+    df2 = chordDiagram(df, plot = FALSE)
+
+    link_count = table(unlist(df))
+
+    for(i in seq_len(nrow(df2))) {
+        s1 = df2[i, 1]
+        s2 = df2[i, 2]
+
+        xlim1 = get.cell.meta.data("xlim", sector.index = s1)
+        df2[i, "x1"] = (df2[i, "x1"] - 0.5)/(link_count[s1]) * (xlim1[2] - xlim1[1]) + xlim1[1]
+        xlim2 = get.cell.meta.data("xlim", sector.index = s2)
+        df2[i, "x2"] = (df2[i, "x2"] - 0.5)/(link_count[s2]) * (xlim2[2] - xlim2[1]) + xlim2[1]
+    }
+    df2 = df2[, c("rn", "cn", "x1", "x2")]
+    colnames(df2) = c("sector1", "sector2", "pos1", "pos2")
+    return(df2)
+}
+

man/arrange_links_evenly.Rd

@@ -0,0 +1,44 @@
+\name{arrange_links_evenly}
+\alias{arrange_links_evenly}
+\title{
+Arrange links evenly on each sector
+}
+\description{
+Arrange links evenly on each sector
+}
+\usage{
+arrange_links_evenly(df)
+}
+\arguments{
+
+  \item{df}{A data frame with two columns. The values should only contain sector names.}
+
+}
+\details{
+This function only deals with single-line links.
+}
+\value{
+A data frame with four columns of the sectors and the positions of the links.
+}
+\examples{
+sectors = letters[1:20]
+df = data.frame(from = sample(sectors, 40, replace = TRUE),
+                to   = sample(sectors, 40, replace = TRUE))
+df = unique(df)
+df = df[df$from != df$to, ]
+
+circos.initialize(sectors, xlim = c(0, 1))
+circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
+    circos.text(CELL_META$xcenter, CELL_META$ycenter, CELL_META$sector.index)
+})
+
+df2 = arrange_links_evenly(df)
+
+for(i in seq_len(nrow(df2))) {
+    s1 = df$from[i]
+    s2 = df$to[i]
+    circos.link(df2[i, "sector1"], df2[i, "pos1"], 
+                df2[i, "sector2"], df2[i, "pos2"],
+                directional = 1)
+}
+}

man/chordDiagramFromDataFrame.Rd

@@ -46,6 +46,7 @@ chordDiagramFromDataFrame(
     group = NULL,
     big.gap = 10,
     small.gap = 1,
+    plot = TRUE,
     ...)
 }
 \arguments{
@@ -88,6 +89,7 @@ chordDiagramFromDataFrame(
   \item{group}{It contains the group labels and the sector names are used as the names in the vector.}
   \item{big.gap}{Gaps between the sectors in the first column of \code{df} and sectors in the second column in \code{df}.}
   \item{small.gap}{Small gap between sectors.}
+  \item{plot}{Internally used.}
   \item{...}{pass to \code{\link{circos.link}}}
 
 }

man/get_most_inside_radius.Rd

@@ -12,4 +12,5 @@ get_most_inside_radius()
 \examples{
 # There is no example
 NULL
+
 }