groupOTU adds an extra group called 0

[MarekGierlinski]

Prerequisites

• [x] Have you read Feedback and follow the guide?
  • [x] make sure your are using the latest release version
  • [x] read the documents
  • [x] google your question/issue

Describe you issue

• [x] Make a reproducible example (e.g. 1)
• [x] your code should contain comments to describe the problem (e.g. what expected and actually happened?)

Ask in right place

• [x] for bugs or feature requests, post here (github issue)
• [x] for questions, please post to google group

Here is a reproducible example to illustrate the issue.

library(tidyverse)
library(ggtree)
library(ape)

set.seed(32)

# 10 nodes, 3 groups
info <- tibble(
  label = paste0("S", 1:10),
  group = c(rep("A", 3), rep("B", 3), rep("C", 4)),
  mean =  c(rep(1, 3), rep(3, 3), rep(5, 4))
)
# group information, a list of three groups, contains node labels
group_info <- split(info$label, info$group)

# create data for clustering: matrix with 10 rows and 30 columns, each row
# contains normal distribution with the mean taken from info tibble
x <- expand_grid(i = 1:30, label = info$label) |> 
  left_join(info, by = "label") |> 
  rowwise() |> 
  mutate(value = rnorm(1, mean)) |> 
  pivot_wider(id_cols = label, names_from = i, values_from = value) |> 
  column_to_rownames("label")

# clustering
hc <- x |> 
  dist() |> 
  hclust()

# convert to phylo, add group information
ph <- ape::as.phylo(hc) 
ph_gr <- groupOTU(ph, group_info)

ggtree(ph_gr, aes(colour = group), layout = "circular", branch.length = "none")

There are three groups, A, B and C, but there is an additional group called 0 in the resulting plot.

I tried to unroot the tree

ph <- ape::unroot(ph)

but this does not help:

[YUE90]

Hello, have you solved it? I also met the same problem now.

[DrZhangjilin]

Hello, have you solved it? I also met the same problem now, too.