diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 93466787..0f582ef9 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 1.5.1 pkgdown_sha: ~ articles: circlize: circlize.html -last_built: 2020-10-14T19:43Z +last_built: 2020-10-18T17:41Z diff --git a/docs/reference/circos.axis.html b/docs/reference/circos.axis.html index 700f13cd..09b85755 100644 --- a/docs/reference/circos.axis.html +++ b/docs/reference/circos.axis.html @@ -226,13 +226,13 @@

See a

https://jokergoo.github.io/circlize_book/book/graphics.html#axes

Examples

- 
factors = letters[1:8]
+    
sectors = letters[1:8]
 circos.par(points.overflow.warning = FALSE)
-circos.initialize(factors = factors, xlim = c(0, 10))
circos.trackPlotRegion(factors = factors, ylim = c(0, 10), track.height = 0.1,
+circos.initialize(sectors, xlim = c(0, 10))
circos.trackPlotRegion(sectors, ylim = c(0, 10), track.height = 0.1,
     bg.border = NA, panel.fun = function(x, y) {
         circos.text(5, 10, get.cell.meta.data("sector.index"))
 })

-circos.trackPlotRegion(factors = factors, ylim = c(0, 10))
circos.axis(sector.index = "a")
circos.axis(sector.index = "b", direction = "inside", labels.facing = "outside")
circos.axis(sector.index = "c", h = "bottom")
circos.axis(sector.index = "d", h = "bottom", direction = "inside",
+circos.trackPlotRegion(sectors, ylim = c(0, 10))
circos.axis(sector.index = "a")
circos.axis(sector.index = "b", direction = "inside", labels.facing = "outside")
circos.axis(sector.index = "c", h = "bottom")
circos.axis(sector.index = "d", h = "bottom", direction = "inside",
     labels.facing = "reverse.clockwise")
circos.axis(sector.index = "e", h = 5, major.at = c(1, 3, 5, 7, 9))
circos.axis(sector.index = "f", h = 5, major.at = c(1, 3, 5, 7, 9),
     labels = c("a", "c", "e", "g", "f"), minor.ticks = 0)
circos.axis(sector.index = "g", h = 5, major.at = c(1, 3, 5, 7, 9),
     labels = c("a1", "c1", "e1", "g1", "f1"), major.tick = FALSE,
@@ -246,8 +246,8 @@ 
Examp
 factors = letters[1]
 
 circos.par("gap.degree" = 0, "cell.padding" = c(0, 0, 0, 0), "start.degree" = 90)
-circos.initialize(factors = factors, xlim = c(0, 12))
-circos.trackPlotRegion(factors = factors, ylim = c(0, 1), bg.border = NA)
+circos.initialize(sectors, xlim = c(0, 12))
+circos.trackPlotRegion(sectors, ylim = c(0, 1), bg.border = NA)
 circos.axis(sector.index = "a", major.at = 0:12, labels = "",
     direction = "inside", major.tick.length = mm_y(3))
 circos.text(1:12, rep(0.5, 12), 1:12, facing = "downward")
diff --git a/docs/reference/circos.initialize.html b/docs/reference/circos.initialize.html
index 77983df0..d6911ce8 100644
--- a/docs/reference/circos.initialize.html
+++ b/docs/reference/circos.initialize.html
@@ -121,10 +121,11 @@ 
Initialize the circular layout

     

 
     
circos.initialize(
-    sectors = NULL, factors = sectors,
+    sectors = NULL,
     x = NULL,
     xlim = NULL,
-    sector.width = NULL)

+    sector.width = NULL,
+    factors = sectors)

 
     
Arguments

     
diff --git a/docs/reference/circos.lines.html b/docs/reference/circos.lines.html
index da0fe8c0..d209ae79 100644
--- a/docs/reference/circos.lines.html
+++ b/docs/reference/circos.lines.html
@@ -215,9 +215,9 @@ 
Details
 area to TURE.

 
     
Examples

-    
factors = letters[1:9]
+    
sectors = letters[1:9]
 circos.par(points.overflow.warning = FALSE)
-circos.initialize(factors = factors, xlim = c(0, 10))
circos.trackPlotRegion(factors = factors, ylim = c(0, 10), track.height = 0.5)

+circos.initialize(sectors, xlim = c(0, 10))
circos.trackPlotRegion(sectors, ylim = c(0, 10), track.height = 0.5)

 circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "a")
circos.text(5, 9, "type = 'l'", sector.index = "a", facing = "outside")

 circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "b", type = "o")
circos.text(5, 9, "type = 'o'", sector.index = "b", facing = "outside")

 circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "c", type = "h")
circos.text(5, 9, "type = 'h'", sector.index = "c", facing = "outside")

diff --git a/docs/reference/circos.par.html b/docs/reference/circos.par.html
index 0870d692..91b97aab 100644
--- a/docs/reference/circos.par.html
+++ b/docs/reference/circos.par.html
@@ -180,8 +180,11 @@ 
Details
  the region. So if some points are out of the plotting region, circlize would continue drawing the points and printing warnings. In some
  cases, draw something out of the plotting region is useful, such as draw
  some legend or text. Set this value to FALSE to turn off the warnings.

-  
circle.margin
Margin in the horizontal direction and in the vertical direction. The value should be a positive numeric vector of length two
- and the values are the fraction to the unit circle. So A value of c(x, y) means circos.par(canvas.xlim = c(-1, 1)*(1+x), canvas.ylim = c(-1, 1)*(1+y)).

+  
circle.margin
Margin in the horizontal and vertical direction. The value should be a positive numeric vector
+ and the length of it should be either 1, 2, or 4. When it has length of 1, it controls the margin on the four sides of the circle.
+ When it has length of 2, the first value controls the margin on the left and right, and the second value controls
+ the margin on the bottom and top side. When it has length of 4, the four values controls the margins on the left, right, bottom and top sides
+ of the circle. So A value of c(x1, x2, y1, y2) means circos.par(canvas.xlim = c(-(1+x1), 1+x2), canvas.ylim = c(-(1+y1), 1+y2)).

   
canvas.xlim
The coordinate for the canvas. Because circlize draws everything (or almost everything) inside the unit circle,
  the default canvas.xlim and canvas.ylim for the canvas would be all c(-1, 1). However, you can set it to a more broad
  interval if you want to draw other things out of the circle. By choosing proper
@@ -218,7 +221,7 @@ 
Examp
 #>  cell.padding            0.02, 1, 0.02, 1
 #>  track.height            0.2             
 #>  points.overflow.warning TRUE            
-#>  circle.margin           0, 0            
+#>  circle.margin           0, 0, 0, 0      
 #>  canvas.xlim             -1, 1           
 #>  canvas.ylim             -1, 1           
 #>  major.by.degree         10              
diff --git a/docs/reference/circos.polygon.html b/docs/reference/circos.polygon.html
index f271dc95..c688dc79 100644
--- a/docs/reference/circos.polygon.html
+++ b/docs/reference/circos.polygon.html
@@ -158,8 +158,8 @@ 
Details
 
     
Examples

     
set.seed(123)
-factors = letters[1:4]
-circos.initialize(factors, xlim = c(0, 1))
circos.trackPlotRegion(ylim = c(-3, 3), track.height = 0.4, panel.fun = function(x, y) {
+sectors = letters[1:4]
+circos.initialize(sectors, xlim = c(0, 1))
circos.trackPlotRegion(ylim = c(-3, 3), track.height = 0.4, panel.fun = function(x, y) {
     x1 = runif(20)
     y1 = x1 + rnorm(20)
     or = order(x1)
diff --git a/docs/reference/circos.rect.html b/docs/reference/circos.rect.html
index 23469e56..5b547e08 100644
--- a/docs/reference/circos.rect.html
+++ b/docs/reference/circos.rect.html
@@ -172,7 +172,7 @@ 
Details
 
This function can be vectorized.

 
     
Examples

-    
circos.initialize(fa = c("a", "b", "c", "d"), xlim = c(0, 10))
circos.track(ylim = c(0, 10), panel.fun = function(x, y) {
+    
circos.initialize(c("a", "b", "c", "d"), xlim = c(0, 10))
circos.track(ylim = c(0, 10), panel.fun = function(x, y) {
     for(rot in seq(0, 360, by = 30)) {
         circos.rect(2, 2, 6, 6, rot = rot)
     }
diff --git a/docs/reference/circos.text.html b/docs/reference/circos.text.html
index 1f436ea9..3f72229e 100644
--- a/docs/reference/circos.text.html
+++ b/docs/reference/circos.text.html
@@ -200,9 +200,9 @@ 
See a
     
https://jokergoo.github.io/circlize_book/book/graphics.html#text

 
     
Examples

-    
factors = letters[1:4]
+    
sectors = letters[1:4]
 circos.par(points.overflow.warning = FALSE)
-circos.initialize(factors = factors, xlim = c(0, 10))
circos.trackPlotRegion(factors = factors, ylim = c(0, 10),
+circos.initialize(sectors, xlim = c(0, 10))
circos.trackPlotRegion(sectors, ylim = c(0, 10),
   track.height = 0.5, panel.fun = function(x, y) {
     circos.text(3, 1, "inside", facing = "inside", cex = 0.8)
     circos.text(7, 1, "outside", facing = "outside", cex = 0.8)
diff --git a/docs/reference/circos.trackHist.html b/docs/reference/circos.trackHist.html
index 5fb1dc80..7e811bad 100644
--- a/docs/reference/circos.trackHist.html
+++ b/docs/reference/circos.trackHist.html
@@ -121,7 +121,7 @@ 
Draw histogram in cells among a whole track

     

 
     
circos.trackHist(
-    sectors, factors = sectors,
+    sectors,
     x,
     track.height = circos.par("track.height"),
     track.index = NULL,
@@ -140,7 +140,8 @@ 
Draw histogram in cells among a whole track

     right = TRUE,
     draw.density = FALSE,
     bin.size = NULL,
-    area = FALSE)

+    area = FALSE,
+    factors = sectors)

 
     
Arguments

     

@@ -242,10 +243,10 @@ 
See a
     
Examples
# \donttest{
 x = rnorm(1600)
-factors = sample(letters[1:16], 1600, replace = TRUE)
-circos.initialize(factors = factors, x = x)
circos.trackHist(factors = factors, x = x, col = "#999999",
-  border = "#999999")
circos.trackHist(factors = factors, x = x, bin.size = 0.1,
-  col = "#999999", border = "#999999")
circos.trackHist(factors = factors, x = x, draw.density = TRUE,
+sectors = sample(letters[1:16], 1600, replace = TRUE)
+circos.initialize(sectors, x = x)
circos.trackHist(sectors, x = x, col = "#999999",
+  border = "#999999")
circos.trackHist(sectors, x = x, bin.size = 0.1,
+  col = "#999999", border = "#999999")
circos.trackHist(sectors, x = x, draw.density = TRUE,
   col = "#999999", border = "#999999")
circos.clear()
 # }

diff --git a/docs/reference/circos.trackLines.html b/docs/reference/circos.trackLines.html
index 67154f47..72b2e3ee 100644
--- a/docs/reference/circos.trackLines.html
+++ b/docs/reference/circos.trackLines.html
@@ -122,7 +122,6 @@ 
Add lines to the plotting regions in a same track
circos.trackLines(
     sectors,
-    factors = sectors,
     x, y,
     track.index = get.current.track.index(),
     col = par("col"),
@@ -136,7 +135,8 @@ 
Add lines to the plotting regions in a same track

     baseline = "bottom",
     pt.col = par("col"),
     cex = par("cex"),
-    pch = par("pch"))

+    pch=par("pch"),
+    factors=sectors)
Arguments

     
   
 
         
 
     
     

diff --git a/docs/reference/circos.trackPlotRegion.html b/docs/reference/circos.trackPlotRegion.html
index 1105df9a..b56f7b00 100644
--- a/docs/reference/circos.trackPlotRegion.html
+++ b/docs/reference/circos.trackPlotRegion.html
@@ -121,7 +121,7 @@ 
Create plotting regions for a whole track
circos.trackPlotRegion(
-    sectors = NULL, factors = sectors,
+    sectors = NULL,
     x = NULL, y = NULL,
     ylim = NULL,
     force.ylim = TRUE,
@@ -133,7 +133,8 @@ 
Create plotting regions for a whole track

     bg.border = "black",
     bg.lty = par("lty"),
     bg.lwd = par("lwd"),
-    panel.fun = function(x, y) {NULL})

+    panel.fun=function(x, y) {NULL},
+    factors=sectors)
Arguments

     
 
         
 
     
     

diff --git a/docs/reference/circos.trackPoints-1.png b/docs/reference/circos.trackPoints-1.png
index 41cad8ee..beede1ff 100644
Binary files a/docs/reference/circos.trackPoints-1.png and b/docs/reference/circos.trackPoints-1.png differ
diff --git a/docs/reference/circos.trackPoints.html b/docs/reference/circos.trackPoints.html
index f394f5b2..6e3cf626 100644
--- a/docs/reference/circos.trackPoints.html
+++ b/docs/reference/circos.trackPoints.html
@@ -122,13 +122,13 @@ 
Add points to the plotting regions in a same track
circos.trackPoints(
     sectors,
-    factors = sectors,
     x, y,
     track.index = get.current.track.index(),
     pch = par("pch"),
     col = par("col"),
     cex = par("cex"),
-    bg = par("bg"))

+    bg=par("bg"),
+    factors=sectors)
Arguments

 
         
 
     
     

@@ -180,9 +180,9 @@ 
Details
 
This function can be replaced by a for loop containing circos.points.

 
     
Examples

-    
circos.initialize(letters[1:8], xlim = c(0, 1))
df = data.frame(fa = sample(letters[1:8], 100, replace = TRUE),
+    
circos.initialize(letters[1:8], xlim = c(0, 1))
df = data.frame(sectors = sample(letters[1:8], 100, replace = TRUE),
                 x = runif(100), y = runif(100))
-circos.track(ylim = c(0, 1))
circos.trackPoints(df$fa, x = df$x, y = df$y, pch = 16, col = as.numeric(factor(df$fa)))
circos.clear()

+circos.track(ylim = c(0, 1))
circos.trackPoints(df$sectors, x = df$x, y = df$y, pch = 16, col = as.numeric(factor(df$fa)))
circos.clear()
circos.trackText(
-    sectors, factors = sectors,
+    sectors,
     x, y,
     labels,
     track.index = get.current.track.index(),
@@ -132,7 +132,8 @@ 
Draw text in cells among the whole track

     adj = par("adj"),
     cex = 1,
     col = par("col"),
-    font = par("font"))

+    font=par("font"),
+    factors=sectors)
Arguments

   
   
 
         
 
     
     

diff --git a/docs/reference/circos.triangle.html b/docs/reference/circos.triangle.html
index c827ac03..9c38b6b8 100644
--- a/docs/reference/circos.triangle.html
+++ b/docs/reference/circos.triangle.html
@@ -157,7 +157,7 @@ 
Arg
 
 
     
Examples

-    
circos.initialize(fa = c("a", "b", "c", "d"), xlim = c(0, 10))
circos.track(ylim = c(0, 10), panel.fun = function(x, y) {
+    
circos.initialize(c("a", "b", "c", "d"), xlim = c(0, 10))
circos.track(ylim = c(0, 10), panel.fun = function(x, y) {
     circos.triangle(c(2, 2), c(2, 8),
                     c(8, 8), c(2, 8),
                     c(5, 5), c(8, 2))
diff --git a/docs/reference/circos.yaxis.html b/docs/reference/circos.yaxis.html
index cd2af2b4..8178906b 100644
--- a/docs/reference/circos.yaxis.html
+++ b/docs/reference/circos.yaxis.html
@@ -200,10 +200,10 @@ 
Details
     
Examples

     
op = par(no.readonly = TRUE)
 
-factors = letters[1:8]
+sectors = letters[1:8]
 circos.par(points.overflow.warning = FALSE)
 circos.par(gap.degree = 8)
-circos.initialize(factors = factors, xlim = c(0, 10))
circos.trackPlotRegion(factors = factors, ylim = c(0, 10), track.height = 0.5)
par(cex = 0.8)
+circos.initialize(sectors, xlim = c(0, 10))
circos.trackPlotRegion(sectors, ylim = c(0, 10), track.height = 0.5)
par(cex = 0.8)
 for(a in letters[2:4]) {
   circos.yaxis(side = "left", sector.index = a)
 }
for(a in letters[5:7]) {