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Problem with agglomerating rowTree #700

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RiboRings opened this issue Mar 5, 2025 · 3 comments
Open

Problem with agglomerating rowTree #700

RiboRings opened this issue Mar 5, 2025 · 3 comments

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@RiboRings
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Hi! There might be a problem with the tree agglomeration (or plotRowTree?)

The tree looks ok with the original tse.

library(mia)
library(miaViz)

data("Tengeler2020")
tse <- Tengeler2020

plotRowTree(tse,
            layout="circular",
            edge_colour_by="Phylum",
            tip_colour_by="Order")
Image

However, after agglomerating the tree looks "disorganised", in the sense that I would still expect taxonomically related taxa to sit closer in the phylogenetic tree as well.

tse_genus <- agglomerateByRank(tse, rank = "Genus")

plotRowTree(tse_genus,
            layout="circular",
            edge_colour_by="Phylum",
            tip_colour_by="Order")
Image
@TuomasBorman
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Very good catch! I will check this in upcoming days.

@RiboRings
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Sorry @ake123 I assigned you by accident!

@TuomasBorman
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markrobinsonuzh/TreeSummarizedExperiment#86

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3 participants
@ake123 @TuomasBorman @RiboRings