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MomX / Momocs

:dove: Morphometrics using R
http://momx.github.io/Momocs/
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fix: correct color order for tip labels and enable to change tip labels #234

Open takosa opened 7 months ago

takosa commented 7 months ago

The coloring by fac argument was incorrect because the order of the factors returned by the fac_dipatcher function was different from the order of the tips(leaves) in dendrograms, which has been corrected. Also, the code for changing tip labels by fac and/or labels arguments was ineffective, which has been corrected.

background

When I was coloring tip labels by fac argument in CLUST function, I noticed that the coloring is constant regardless of the topology of dendrograms. As an example, I ran the following code and found that there was a discrepancy between the tip labels and the colors.

hearts |> efourier() |> CLUST(fac=~aut) + coord_flip(xlim=c(25,35))

This may be due to the fact that the following code specifies the return value of fac_dispatcher as it is, when it should specify the colors in the same order as tip labels.

f <- fac_dispatcher(x, fac)
d %<>% dendextend::set("labels_colors",
                       palette(nlevels(f))[f])

Also, the following code seems to intend to change labels appropriately when fac or labels arguments are specified, but to no effect. It seems that this needs to be corrected appropriately as well.

# handle labels (could be shortened)
dendextend::`labels<-`(d, names(x))
if (!missing(fac) && !is.null(fac))          # if fac is provided, use it
  dendextend::`labels<-`(d, as.character(fac_dispatcher(x, fac)))
if (!missing(labels) && !is.null(labels))      # but if labels is provided, overwrite it
  dendextend::`labels<-`(d, as.character(fac_dispatcher(x, labels)))