Circular dendrogram

[andrie]

Suggested enhancement by Ulrik Stervbo

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Hi Andrie,

Thanks for taking the time with the ggdendro package.

I wanted to plot a circular dendrogram and was unhappy with the implementation in Ape (the leaf order is mirrored). I realized I could achieve my goal by modifying the segments of the dendro_data result and use the coord_polar().

The benefit is, that the dendrogram can then be "downwards" and "rightwards" (the two current variations with rotate = FALSE and rotate=TRUE respectively) but also "upwards" and "leftwards" (to stay in the terminology from ape).

To achieve the last two variants I simply modified the y-values:

hcdata$segments[["y"]] <- abs(hcdata$segments[["y"]] - max(hcdata$segments[["y"]]))
hcdata$segments[["yend"]] <- abs(hcdata$segments[["yend"]] - max(hcdata$segments[["yend"]]))

Example:

hc <- hclust(dist(USArrests), "ave")
plot(hc)
### demonstrate converting hclust to dendro using dendro_data first
hcdata <- dendro_data(hc)
ggdendrogram(hcdata, rotate=FALSE, size=2) + labs(title="Dendrogram in ggplot2 - Rotate=F; segments not modified; downwards")
ggdendrogram(hcdata, rotate=TRUE, size=2) + labs(title="Dendrogram in ggplot2 - Rotate=T; segments not modified; rightwards")


hcdata$segments[["y"]] <- abs(hcdata$segments[["y"]] - max(hcdata$segments[["y"]]))
hcdata$segments[["yend"]] <- abs(hcdata$segments[["yend"]] - max(hcdata$segments[["yend"]]))

ggdendrogram(hcdata, rotate=TRUE, size=2) + labs(title="Dendrogram in ggplot2- Rotate=T; segments modified; leftwards")
ggdendrogram(hcdata, rotate=FALSE, size=2) + labs(title="Dendrogram in ggplot2- Rotate=F; segments modified; upwards")

ggdendrogram(hcdata) + labs(title="Dendrogram in ggplot2 - Fan") + coord_polar()

May I suggest you deprecate the rotate and replace it with a direction = c("downwards", "upwards", "rightwards", "leftwards") and add a type = c("phylogram", "fan").

if the type is fan, then the above modification is performed and the returned plot is simply

ggdendrogram() + coord_polar()

Please let me know if something is not clear. I could also extend the code, but I dont want to make too much of a mess.

All the best, Ulrik

[andrie]

There are two problems in implementing this:

• ggplot2 doesn't allow for axes to be at top or right of plot area. Thus, as currently imlemented, the leaf labels get disconnected from the segments.
• To implement the fan plot, one will have to (somehow) specify individual rotation of the leaf labels in the axis.

Thus an implementation requires a modification of ggdendrogram() to use text labels rather than axis labels.

[talgalili]

Hi @andrie, Since ggdend (from the dendextend package) works with geom_text, it supports the fan plot, you can see it here: https://cran.r-project.org/web/packages/dendextend/vignettes/introduction.html#ggplot2-integration

Also, it is worth noting the wonderful package "circlize", which deals with creating fan plots (also of dendrograms). For more simpler cases, dendextend offers a wrapper called circlize_dendrogram, which gives a fan plot "out of the box" for a dendrogram (but in base R, not ggplot2). You can see an example for it here: https://cran.r-project.org/web/packages/dendextend/vignettes/introduction.html#circlize

Cheers, Tal

[jbkunst]

Hi @andrie,

First of all nice package! I think I'll use your package to chart dendrograms in highcharter via the generic function hchart(http://jkunst.com/highcharter/hchart.html). What will you do with this issue? To know if I implement the Ulrik idea or wait some changes in ggdendro.

Finally, no phylo?

Regards.