CODEWITHSUNDEEP
rggplot2dendrogramdendextend
cs-
cs-

Reputation: 21

best way to convert dendrogram to ggplot?

I have build up a dendrogram and colored its branches according to their "purity" (whether they only include subjects with a particular value in a factor variable) using the set("by_labels_branches_col") function of the dendextend package. Now, I would like to convert this dendrogram to a ggplot2 object for further customization. I have been able to do that with the function as.ggdend (also from the dendextend package). Here is when I encounter 2 issues for which I would need some help:

1-After using as.ggdend, the resulting object "loses" the vertical axis indicating the height of the dendrogram... How could I do this transformation without losing the axis?

2.-I have also tried to enrich my dendrogram by adding a colored bar using the colored_bars function of the dendextend package. However, I do not know how to save the resulting object to convert it to a ggplot object.

Here I provide an example of my code with the mtcars dataset

df=mtcars
ds=dist(df, "euclidean")
hc<-hclust(ds,method= "average")
de=as.dendrogram(hc)
library(dendextend)
code=rownames(df[df$cyl==4,])#factor for coloring
de2<-de%>%set("by_labels_branches_col", value = c(code))%>% set("labels", "")%>%as.dendrogram(de)#coloring branches
#to add the colored bar
colores<-c("red","black", "blue") [as.factor(df$cyl)]
plot(de2)
colored_bars(colors=colores,dend=de2, y_shift=-2, rowLabels="" )
#transform to ggplot
de3=as.ggdend(de2)

Thanks in advance for any possible answer

Upvotes: 1

Views: 501

Answers (1)

cs-
cs-

Reputation: 21

Finally, I have found a solution for the first of the posted questions). It is far from elegant and probably there are better ways to do this. However, I post it here just in case someone finds it useful.

The solution skips the use of as.ggdend and directly uses ggplot+theme to ensure that the dendrogram axis is displayed. Because this automatically thickens all plot lines, line sizes are corrected at steps 2/3.

step1=ggplot(de2)+
    theme(axis.line.y = element_line(color="black"),
    axis.text.y = element_text(color="black"),
    axis.ticks.y = element_line(color="black"))+
    scale_y_continuous(expand = expansion(add = c(0,0)))
    
    step2=ggplot_build(step1)
    step2$data[[1]]$size=0.3

    step3= ggplot_gtable(step2)

    step4=ggplotify::as.ggplot(step3)

Upvotes: 1

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