Two question about import qiime2 files

[Rainjie-afk]

Hello! Very nice work!
I'm looking for help with running qiime2 files as import files (contain tree file) :

test_files <- import_qiime2("T2DM_16S_Amplificateion_import_results_table-dada2.qza",
                            taxaqza = "T2DM_16S_Amplificateion_import_results_import_results-rep-seqs_gtdb-214-bacteria-v3v4-classifier.qza",
                            mapfilename = "Group_metadata2.tsv",
                            treeqza = "T2DM_16S_Amplificateion_import_results_import_results-rep-seqs-aligned-masked-fasttree-tree")
mpse <- test_files %>% as.mpse()
mpse
# A MPSE-tibble (MPSE object) abstraction: 331,360 × 12
# OTU=8284 | Samples=40 | Assays=Abundance | Taxonomy=Kingdom, Phylum, Class, Order, Family, Genus, Speies
   OTU                              Sample Abundance Num   Group Kingdom        Phylum           Class Order Family Genus Speies
   <chr>                            <chr>      <dbl> <chr> <chr> <chr>          <chr>            <chr> <chr> <chr>  <chr> <chr> 
 1 3d465cca97074831971c7a7ccd5da390 F_103        229 DM_1  DM    k__d__Bacteria p__p__Desulfoba… c__c… o__o… f__f_… g__g… s__s_…
 2 a16720e62eebc35341b4fe472c181960 F_103        222 DM_1  DM    k__d__Bacteria p__p__Desulfoba… c__c… o__o… f__f_… g__g… s__s_…
 3 38257b864b5c8a324287642894f70ba8 F_103        150 DM_1  DM    k__d__Bacteria p__un_k__d__Bac… c__u… o__u… f__un… g__u… s__un…
 4 d1e1de8b48805bc64d71f66d1de798a1 F_103        163 DM_1  DM    k__d__Bacteria p__p__Desulfoba… c__c… o__o… f__f_… g__g… s__s_…
 5 ddc1d84b71dcf973e2f2c4150b51d297 F_103        137 DM_1  DM    k__d__Bacteria p__un_k__d__Bac… c__u… o__u… f__un… g__u… s__un…
 6 d248201d0fd2e84c22df158bb7b12e14 F_103         86 DM_1  DM    k__d__Bacteria p__p__Bacillota  c__c… o__o… f__f_… g__g… s__un…
 7 40f5617dbc353f11123252dae526a1ec F_103        140 DM_1  DM    k__d__Bacteria p__p__Bacillota  c__c… o__o… f__f_… g__g… s__un…
 8 cb8bdefd71370ab957076bdd3e3c9a05 F_103        118 DM_1  DM    k__d__Bacteria p__un_k__d__Bac… c__u… o__u… f__un… g__u… s__un…
 9 c53726cfa32814f54fca8f3034b87ace F_103        125 DM_1  DM    k__d__Bacteria p__un_k__d__Bac… c__u… o__u… f__un… g__u… s__un…
10 282c6376e49a5757828b0ba26bbfa875 F_103        120 DM_1  DM    k__d__Bacteria p__un_k__d__Bac… c__u… o__u… f__un… g__u… s__un…
# ℹ 331,350 more rows
# ℹ Use `print(n = ...)` to see more rows

1. 2.8 Performing differential analysis among multiple groups
   How can i delete nodes which can't identify in the level which i selected?
   mpse2_4groups %>% mp_rrarefy() %>% mp_diff_analysis(.abundance=RareAbundance, .group=Group) %>% mp_extract_tree(tip.level=Fanmily) -> taxa.tree

PS.
I have try code like this taxa.tree %>% dplyr::filter(!grepl("^g__un_o|^g__un_f",label)), but it doesn't work

2. The second question related to the first one:

The code runs smoothly until chapter 2.7 "Significant differential clades for the diagnosis of some related diseases"

mpse3 %>% mp_balance_clade( .abundance = Abundance, force = TRUE, relative = FALSE, pseudonum = 1, balance_fun='geometric.mean' ) -> mpse.balance.node
R Console tells me that I should use ape to load tree file which made me can't run any further.

So, is there any way to solve this problem?
Perhaps I should run mp_extract_tree(), but i really run out of idea, help me please.

[Rainjie-afk]

Another tiny question occured when i run mpse16s %<>% dplyr::left_join(sample.da, by=c("Sample"="sample_id")) in chapter 3.1 The parsing of the 16s data and construction of MPSE class
dplyr::left_join seems unable to match Sample in mpse16s

> mpse16s %<>% dplyr::left_join(sample.da, by=c("Sample"="sample_id"))


> rlang::last_trace()
<error/rlib_error_dots_nonempty>
Error in `left_join()`:
! `...` must be empty.
✖ Problematic argument:
• ..1 = !!!dots
ℹ Did you forget to name an argument?
---
Backtrace:
    ▆
 1. ├─mpse16s %<>% dplyr::left_join(sample.da, by = c(Sample = "sample_id"))
 2. ├─dplyr::left_join(., sample.da, by = c(Sample = "sample_id"))
 3. ├─MicrobiotaProcess:::left_join.MPSE(., sample.da, by = c(Sample = "sample_id"))
 4. │ └─sampleda %>% ...
 5. ├─dplyr::left_join(...)
 6. └─dplyr:::left_join.data.frame(., y, by = by, copy = copy, suffix = suffix, !!!dots)
Run rlang::last_trace(drop = FALSE) to see 5 hidden frames.
> mpse16s %<>% dplyr::left_join(sample.da, by=c("Sample"="sample_id"), !!!dots)
Error in `left_join()`:
! `...` must be empty.
✖ Problematic argument:
• ..1 = !!!dots
ℹ Did you forget to name an argument?

Is there any way to bypass left_join when I want to load PICRUST2 result and group_metadata to generate MPSE object?

[Rainjie-afk]

Inspire by this post https://github.com/YuLab-SMU/MicrobiotaProcess/issues/43

The following method can solve the sorting error in multiple groups:

taxa.tree %>% 
  dplyr::filter(nodeClass=="Phylum" & !is.na(Sign_Group), keep.td=FALSE) -> genus.tb
genus.tb %>% 
  tidyr::unnest(RareAbundanceBySample) %>% 
  dplyr::filter(!grepl("^f__un_", label)) -> df_taxa.tree_Phylum
df_taxa.tree_Phylum$Group <- factor(df_taxa.tree_Phylum$Group, 
                                    levels = c("NC","DM","DL","DH"))
cols_2 <- rev(cols)
df_taxa.tree_Phylum %>% ggplot(aes(y=label, x =RelRareAbundanceBySample, fill=Group)) + 
  geom_boxplot(orientation='y', outlier.colour = NA) + 
  scale_fill_manual(values = cols_2) +
  ylab(NULL) + theme(legend.key = element_blank()) -> a1