The plot generated by the 'plot_diff_cladogram' function appears unusual and difficult to interpret.

[lzuChengweiZhang]

Dear friends:
Hi! Thank you so much for developing this amazing and useful package!

However, I am encountering an issue with the cladogram generated by the plot_diff_cladogram function during my LEfSe analysis.

I have attached my cladogram here:
LEfSe_phylo.pdf

As you can see, the plot is highly unusual. All the nodes are clustered together in a small central circle, causing significant overlap and making it difficult to distinguish between them.

I can't figure out where the problem lies because I am following the tutorial from here, which is the official website of the package tutorials.

Here is my process:

1. IMPORT THE DATA TO THE MICROECO
   data_micro <- microtable$new(sample_table = df_tumor_health_tissue, otu_table = df_genus_tissue_t, tax_table = df_taxa_genus)
   My datasets are attached here.
   otu_table.csv
   tax_table.csv
   sample_table.csv
2. PERFORMING LEFSE ANALYSIS
   t1 <- trans_diff$new(dataset = data_micro, method = "lefse", group = "Type", alpha = 0.05, lefse_subgroup = NULL)
   The "Type" column is composed by two elements: PC and EC.
3. PLOTTING DIFFERENT BAR PLOT
   t1$plot_diff_bar(threshold = 4)
   The plot looks like quite normal.
   
4. PLOTTING CLADOGRAM
   This is where the things went wrong. I used following code to generate a cladogram of my group: PC and EC.
   t1$plot_diff_cladogram(use_taxa_num = 100, use_feature_num = 50, clade_label_level = 5, group_order = c('EC', 'PC'))
   But the result is abnormal and confusing. I am strictly following the tutorial but have a very confusing result. I don't have any clues so far about the issue.

Thank you in advance for your help!

[ChiLiubio]

Hi. Please first try to run the following codes and then perform lefse. I guess it is the reason of taxonomic information.

library(magrittr)
data_micro$tax_table %<>% tidy_taxonomy
data_micro$tidy_dataset()
data_micro$cal_abund()

If the issue is still there, please use save function to save your data_micro and attach the compressed data so that I can totally and easily reproduce your issue. To save data_micro, please follow the tutorial (https://chiliubio.github.io/microeco_tutorial/notes.html#save-function)

[lzuChengweiZhang]

Dear Liubio
Hi, Thank you very much for your reply and solutions!

I have tried the codes to tidy my taxonomic information and try again to run plot_diff_cladogram. Finally, it works! I got the right picture!

I found that taxonomic information need the prefixes such as "f__", "g__" and "s__" as taxonomy markers, which I was neglected and thus caused the trouble.

By the way, I am also Chinese and currently pursuing my master's degree in Lanzhou. If you ever travel here, I would be pleased to treat you to beef noodles and be your tour guide!

Thank you again for your help! It truly helped me a lot!

[ChiLiubio]

好的，感谢！有机会了去兰州玩