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
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.nef at 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 at 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]]
Yes I know. Sorry if I reposted this but it's simply because I've received an email mentioning that the file was too big that's why I modified my question and reposted it. I don't want to oblige anyone to respond. I really thought the issue was my file (too big so nobody received it). Thanks for your understanding, Best Myriam On Fri, Jan 11, 2019 at 3:03 PM Bert Gunter <bgunter.4567 at gmail.com> wrote:> > 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.nef at 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 at 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.-- Meriam Nefzaoui MSc. in Plant Breeding and Genetics Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil