export get_most_inside_radius()

DESCRIPTION

@@ -2,7 +2,7 @@ Package: circlize
 Type: Package
 Title: Circular Visualization
 Version: 0.4.12
-Date: 2020-10-18
+Date: 2020-11-23
 Author: Zuguang Gu
 Maintainer: Zuguang Gu <[email protected]>
 Depends: R (>= 3.0.0), graphics

NAMESPACE

@@ -84,6 +84,7 @@ export("get.current.chromosome")
 export("get.current.sector.index")
 export("get.current.track.index")
 export("getI")
+export("get_most_inside_radius")
 export("highlight.chromosome")
 export("highlight.sector")
 export("inch_h")

NEWS

@@ -8,6 +8,8 @@ Changes in version 0.4.12
 * `circos.link()`: add a new `inverse` argument to control whether the link
   is inversed or not.
 * `circos.genomicLabels()`: replace `side` argument with `labels.side`.
+* `circos.points()`, `circos.lines()`, `circos.text()` allow argument `x` to be
+  a two-column matrix.
 
 Changes in version 0.4.11
 -----------------------------------------------------------------------

R/link.R

@@ -99,15 +99,15 @@ circos.link = function(
 
 		d = getQuadraticPoints(theta1, theta2, rou1, rou2, h = h, h.ratio = h.ratio, w = w)
         nr = nrow(d)
-        if(directional == 0) {
+        # if(directional == 0) {
         	lines(d, col = col, lwd = lwd, lty = lty, lend = "butt")
-        } else if(directional == 1) {
-			lines(d[-nr, , drop = FALSE], col = col, lwd = lwd, lty = lty, lend = "butt")
-		} else if(directional == -1) {
-			lines(d[-1, , drop = FALSE], col = col, lwd = lwd, lty = lty, lend = "butt")
-		} else if(directional == 2) {
-			lines(d[-c(1, nr), , drop = FALSE], col = col, lwd = lwd, lty = lty, lend = "butt")
-		}
+  #       } else if(directional == 1) {
+		# 	lines(d[-nr, , drop = FALSE], col = col, lwd = lwd, lty = lty, lend = "butt")
+		# } else if(directional == -1) {
+		# 	lines(d[-1, , drop = FALSE], col = col, lwd = lwd, lty = lty, lend = "butt")
+		# } else if(directional == 2) {
+		# 	lines(d[-c(1, nr), , drop = FALSE], col = col, lwd = lwd, lty = lty, lend = "butt")
+		# }
 
         if(nrow(d) > 1) {
 	        if(directional %in% c(1,2)) {  # point1 to point2

R/low_level.R

@@ -52,6 +52,13 @@ circos.points = function(
         stop_wrap("'circos.points' can only be used after the plotting region has been created")
     }
 
+    if(missing(y)) {
+        if(ncol(x) == 2) {
+            y = x[, 2]
+            x = x[, 1]
+        }
+    }
+
     len_x = length(x)
     len_y = length(y)
     if(len_x == 1) x = rep(x, len_y)
@@ -238,6 +245,13 @@ circos.lines = function(
 		warning_wrap("`area.baseline` is deprecated, please use `baseline` instead.")
 	}
 
+    if(missing(y)) {
+        if(ncol(x) == 2) {
+            y = x[, 2]
+            x = x[, 1]
+        }
+    }
+
 	if(length(x) != length(y)) {
 		stop_wrap("Length of x and y differ.")
 	}
@@ -841,6 +855,14 @@ circos.text = function(
 	font = par("font"),
 	...) {
 
+
+    if(missing(y)) {
+        if(ncol(x) == 2) {
+            y = x[, 2]
+            x = x[, 1]
+        }
+    }
+
     len_x = length(x)
     len_y = length(y)
     if(len_x == 1) x = rep(x, len_y)

R/utils.R

@@ -428,6 +428,9 @@ add_transparency = function (col, transparency = 0) {
     rgb(t(col2rgb(col)/255), alpha = 1 - transparency)
 }
 
+# == title
+# Get the inside radius of the most inner track
+#
 get_most_inside_radius = function() {
 	tracks = get.all.track.index()
 	if(length(tracks) == 0) {
@@ -1137,7 +1140,7 @@ message_wrap = function(...) {
 
 validate_data_frame = function(x) {
     if(inherits(x, "data.frame")) {
-        return(x)
+        return(as.data.frame(x))
     } else if(inherits(x, "GRanges")) {
         x = as.data.frame(x)
         return(x[, -(4:5), drop = FALSE])

man/get_most_inside_radius.Rd

@@ -0,0 +1,15 @@
+\name{get_most_inside_radius}
+\alias{get_most_inside_radius}
+\title{
+Get the inside radius of the most inner track
+}
+\description{
+Get the inside radius of the most inner track
+}
+\usage{
+get_most_inside_radius()
+}
+\examples{
+# There is no example
+NULL
+}