Can you help me with plot_diff_cladogram?

[CTTST]

When I was following the 6.1 trans_diff class, I found my cladogram does not have any annotation on it, which is different from the cladogram in the tutorial. Can you please help me find out what the problem is? Thx!!

• Here is the data: test_data.zip
• Here is the codes:

packageVersion("ggtree")
# [1] ‘3.8.2’

library(microeco)

t1 <- trans_diff$new(dataset = dataset,
                     method = "lefse",
                     group = "Group",
                     alpha = 0.01,
                     lefse_subgroup = NULL)
t1$plot_diff_cladogram(use_taxa_num = 200,
                       use_feature_num = 50,
                       clade_label_level = 5,
                       group_order = c("CW", "IW", "TW"))

# The console shows that there are warnings, 
# so I use warnings() to see the messages as follows
warnings()
# Warning messages:
#   1: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 2: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 3: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 4: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 5: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 6: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 7: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 8: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 9: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 10: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 11: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 12: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 13: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 14: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 15: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 16: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 17: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 18: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 19: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 20: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 21: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 22: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 23: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 24: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 25: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 26: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 27: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 28: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 29: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 30: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 31: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 32: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 33: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 34: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 35: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 36: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 37: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 38: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 39: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 40: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 41: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 42: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 43: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 44: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 45: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 46: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 47: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 48: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 49: Computation failed in `stat_clad_bar()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"
# 50: Computation failed in `stat_clade_text()`
# Caused by error in `offspring.tbl_tree_item()`:
#   ! could not find function "offspring.tbl_tree_item"

[ChiLiubio]

Hi,
I found this is an extremely confusing issue. At first, I used my ggtree v3.8.0 to run these steps and found it is fine. Then I updated ggtree to the version v3.8.2 that you used. Then I got your result! But when I debug the steps, I found the issue may come from the initial ggtree function, which may come from the compatibility issue of dependent packages. So then I updated all the dependent packages and the issue is still there. Then I debug it step by step, but the issue disappear! Then no matter how I run the steps, the issue can not be reproduced！ So I think it is probably the dependent packages loading sequence problem, which may lead to the function overwritten. Now please update these packages and try again.

Please feel free to tell me if it is still there. Thanks.

Best,
Chi

[vrmarcelino]

I had a similar issue.
Loading the tidytree functions as specified here worked for me:
YuLab-SMU/enrichplot#249 (comment)

[ChiLiubio]

@vrmarcelino Thanks for providing this source!