Overlapping legend in a circular dendrogram
Hi Meriam, I don't have the packages loaded that you use, but a first guess would be to start a wider device. For example, the default x11 device is 7x7, so: x11(width=10) would give you a rectangular output device that might move the columns of labels outward. The same applies for any other device, just explicitly open the wider device before you run your code. Jim
On Sat, Jan 12, 2019 at 3:29 AM N Meriam <meriam.nef at gmail.com> wrote:
Dear all,
I run the following code and I get this graphic (pdf attached). What should
I change in my code in order to adjust the overlapping objects?
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)
Thanks,
Meriam
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