This is the 3rd time you've posted this. Please stop re-posting!
Your question is specialized and involved, and you have failed to provide a
reproducible example/data. We are not obliged to respond.
You may do better contacting the maintainer, found by ?maintainer, as
recommended by the posting guide for specialized queries such as this.
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Fri, Jan 11, 2019 at 12:47 PM N Meriam <meriam....@gmail.com> wrote:
> Hi, I'm facing some issues when generationg a circular dendrogram.
> The labels on the left which are my countries are overlapping with the
> circular dendrogram (middle). Same happens with the labels (regions)
> located on the right.
> I run the following code and I'd like to know what should be changed
> in my code in order to avoid that.
>
> load("hc1.rda")
> library(cluster)
> library(ape)
> library(dendextend)
> library(circlize)
> library(RColorBrewer)
>
> labels = hc1$labels
> n = length(labels)
> dend = as.dendrogram(hc1)
> markcountry=as.data.frame(markcountry1)
> #Country colors
> groupCodes=as.character(as.factor(markcountry[,2]))
> colorCodes=rainbow(length(unique(groupCodes))) #c("blue","red")
> names(colorCodes)=unique(groupCodes)
> labels_colors(dend) <- colorCodes[groupCodes][order.dendrogram(dend)]
>
> #Region colors
> groupCodesR=as.character(as.factor(markcountry[,3]))
> colorCodesR=rainbow(length(unique(groupCodesR))) #c("blue","red")
> names(colorCodesR)=unique(groupCodesR)
>
> circos.par(cell.padding = c(0, 0, 0, 0))
> circos.initialize(factors = "foo", xlim = c(1, n)) # only one sector
> max_height = attr(dend, "height") # maximum height of the trees
>
> #Region graphics
> circos.trackPlotRegion(ylim = c(0, 1.5), panel.fun = function(x, y) {
> circos.rect(1:361-0.5, rep(0.5, 361), 1:361-0.1, rep(0.8,361), col =
> colorCodesR[groupCodesR][order.dendrogram(dend)], border = NA)
> }, bg.border = NA)
>
> #labels graphics
> circos.trackPlotRegion(ylim = c(0, 0.5), bg.border = NA,
> panel.fun = function(x, y) {
>
> circos.text(1:361-0.5,
> rep(0.5,361),labels(dend), adj = c(0, 0.5),
> facing = "clockwise", niceFacing =
> TRUE,
> col = labels_colors(dend), cex =
> 0.45)
>
> })
> dend = color_branches(dend, k = 6, col = 1:6)
>
> #Dendrogram graphics
> circos.trackPlotRegion(ylim = c(0, max_height), bg.border = NA,
> track.height = 0.4, panel.fun = function(x, y) {
> circos.dendrogram(dend, max_height = 0.55)
> })
>
> legend("left",names(colorCodes),col=colorCodes,text.col=colorCodes,bty="n",pch=15,cex=0.8)
>
> legend("right",names(colorCodesR),col=colorCodesR,text.col=colorCodesR,bty="n",pch=15,cex=0.35)
>
> Cheers,
> Myriam
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
