add 'area' argument in 'circos.trackHist()'

jokergoo · Nov 20, 2017 · c00a39b · c00a39b
1 parent 6129c3b
commit c00a39b
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Showing 4 changed files with 9 additions and 4 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -96,6 +96,7 @@ importFrom("colorspace", XYZ)
 importFrom("colorspace", coords)
 importFrom("colorspace", hex)
 importFrom("colorspace", sRGB)
+importFrom("grDevices", "dev.cur", "dev.prev", "dev.set")
 importFrom("grDevices", "dev.off", "pdf")
 importFrom("grDevices", as.raster)
 importFrom("grDevices", col2rgb)
@@ -107,4 +108,4 @@ importFrom("stats", rnorm)
 importFrom("stats", runif)
 importFrom("utils", download.file)
 importFrom("utils", read.table, packageDescription)
-importFrom("grDevices", "dev.cur", "dev.prev", "dev.set")
+
diff --git a/NEWS b/NEWS
@@ -1,6 +1,8 @@
 Changes in version 0.4.3
 --------------------------------------------------------------------------
 
+* `circos.trackHist()`: add `area` argument to add filled color under density lines.
+
 Changes in version 0.4.2
 ---------------------------------------------------------------------------
 

diff --git a/R/plot.R b/R/plot.R
@@ -1584,6 +1584,7 @@ circos.yaxis = function(side = c("left", "right"), at = NULL, labels = TRUE, tic
 # -include.lowest see `graphics::hist`
 # -right          see `graphics::hist`
 # -draw.density   whether draw density lines instead of histogram bars.
+# -area           whether to fill the area below the density lines. If it is set to ``TRUE``, ``col`` controls the filled color in the area and ``border`` controls color of the line. 
 # -bin.size size of the bins of the histogram
 # 
 # == details
@@ -1594,7 +1595,7 @@ circos.trackHist = function(factors, x, track.height = circos.par("track.height"
 	border = "black", lty = par("lty"), lwd = par("lwd"),
     bg.col = NA, bg.border = "black", bg.lty = par("lty"), bg.lwd = par("lwd"),
     breaks = "Sturges", include.lowest = TRUE, right = TRUE, draw.density = FALSE,
-    bin.size = NULL) {
+    bin.size = NULL, area = FALSE) {
 
     # basic check here
     if(length(x) != length(factors)) {
@@ -1662,7 +1663,7 @@ circos.trackHist = function(factors, x, track.height = circos.par("track.height"
 
     if(draw.density) {
         circos.trackLines(factors = fa, xx, yy, track.index = track.index,
-                          col = col, lty = lty, lwd = lwd)
+                          col = col, lty = lty, lwd = lwd, area = area, border = border)
     } else {
         # in each cell, draw rectangles
         col = recycle.with.levels(col, le)

diff --git a/man/circos.trackHist.rd b/man/circos.trackHist.rd
@@ -12,7 +12,7 @@ circos.trackHist(factors, x, track.height = circos.par("track.height"),
     border = "black", lty = par("lty"), lwd = par("lwd"),
     bg.col = NA, bg.border = "black", bg.lty = par("lty"), bg.lwd = par("lwd"),
     breaks = "Sturges", include.lowest = TRUE, right = TRUE, draw.density = FALSE,
-    bin.size = NULL)
+    bin.size = NULL, area = FALSE)
 }
 \arguments{
 
@@ -33,6 +33,7 @@ circos.trackHist(factors, x, track.height = circos.par("track.height"),
   \item{include.lowest}{see \code{\link[graphics]{hist}}}
   \item{right}{see \code{\link[graphics]{hist}}}
   \item{draw.density}{whether draw density lines instead of histogram bars.}
+  \item{area}{whether to fill the area below the density lines. If it is set to \code{TRUE}, \code{col} controls the filled color in the area and \code{border} controls color of the line. }
   \item{bin.size}{size of the bins of the histogram}
 
 }