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ChiLiubio / microeco

An R package for data analysis in microbial community ecology
GNU General Public License v3.0
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Can you help me with plot_diff_cladogram? #279

Closed CTTST closed 5 months ago

CTTST commented 9 months ago
image

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!!

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 commented 9 months ago

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. 1696665586301

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

Best, Chi

vrmarcelino commented 4 months ago

I had a similar issue. Loading the tidytree functions as specified here worked for me: https://github.com/YuLab-SMU/enrichplot/issues/249#issuecomment-1787431446

ChiLiubio commented 4 months ago

@vrmarcelino Thanks for providing this source!