[R] Fwd: Overlapping legend in a circular dendrogram

[Bert Gunter]

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Bert Gunter

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On Fri, Jan 11, 2019 at 12:47 PM N Meriam <meriam.nef using 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
>
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