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rarefaction for first quartile?

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
r
Domain
data

Research direction

Start by reproducing the reported workflow with mp_cal_rarecurve(), as.MPSE(), and mp_plot_rarecurve() using the supplied Abundance and Observe arguments. Trace where the plotting entry point selects the assay column, then confirm that first-quartile rarefaction and the downstream rarefaction curve work without the reported missing-column error.

Written by the indexing model from the issue text.

Description

I want to rarefy my samples to the first quartile.
i don't understand how mp_cal_rarecurve() works with this?

mouse.time.mpse %<>% 
    mp_cal_rarecurve(
        .abundance = RareAbundance,
        chunks = 400
    )

I tried to do the rarefaction before converting my phyloseq to mpse but I could not go futher the downstream analysis from there as I get an error

summary(sample_sums(ps.prev))
ps.prev.rare <- rarefy_even_depth(ps.prev, sample.size = 3501, rngseed = 50)
  Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    641    3501   20304   52969   68311  321517 
`set.seed(50)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(50); .Random.seed` for the full vector
...
32 samples removedbecause they contained fewer reads than `sample.size`.
Up to first five removed samples are: 

M-T1-Rep4M-T5-Rep2M-T5-Rep3M-T5-Rep4M-T5-Rep6
...
2025OTUs were removed because they are no longer 
present in any sample after random subsampling
mpse.rare <- ps.prev.rare %>% as.MPSE()
mpse.rare %>% print(width=180)
# A MPSE-tibble (MPSE object) abstraction: 286,732 × 20
# OTU=2956 | Samples=97 | Assays=Abundance | Taxonomy=Kingdom, Phylum, Class, Order,
#   Family, Genus, Species
   OTU   Sample      Abundance sample.name sample.no Sample.x Phase Region Regime
   <chr> <chr>           <dbl> <chr>           <int> <fct>    <fct> <fct>  <fct> 
 1 ASV1  feed-M-Rep1         6 M1                170 feed     feed  feed   M     
 2 ASV3  feed-M-Rep1       424 M1                170 feed     feed  feed   M     
 3 ASV5  feed-M-Rep1         0 M1                170 feed     feed  feed   M     
 4 ASV6  feed-M-Rep1         0 M1                170 feed     feed  feed   M     
 5 ASV7  feed-M-Rep1         0 M1                170 feed     feed  feed   M     
 6 ASV8  feed-M-Rep1         0 M1                170 feed     feed  feed   M     
 7 ASV9  feed-M-Rep1         0 M1                170 feed     feed  feed   M     
 8 ASV10 feed-M-Rep1         0 M1                170 feed     feed  feed   M     
 9 ASV11 feed-M-Rep1         0 M1                170 feed     feed  feed   M     
10 ASV12 feed-M-Rep1         0 M1                170 feed     feed  feed   M     
   Sample_Regime sample_regime sample sample_or_control Kingdom    
   <fct>         <chr>         <chr>  <chr>             <chr>      
 1 feed.M        feed.M        feed   sample            k__Bacteria
 2 feed.M        feed.M        feed   sample            k__Bacteria
 3 feed.M        feed.M        feed   sample            k__Bacteria
 4 feed.M        feed.M        feed   sample            k__Bacteria
 5 feed.M        feed.M        feed   sample            k__Bacteria
 6 feed.M        feed.M        feed   sample            k__Bacteria
 7 feed.M        feed.M        feed   sample            k__Bacteria
 8 feed.M        feed.M        feed   sample            k__Bacteria
 9 feed.M        feed.M        feed   sample            k__Bacteria
10 feed.M        feed.M        feed   sample            k__Bacteria
   Phylum               Class                  Order               Family Genus Species
   <chr>                <chr>                  <chr>               <chr>  <chr> <chr>  
 1 p__Firmicutes        c__Clostridia          o__Oscillospirales  f__Ru… g__u… s__un_…
 2 p__Firmicutes        c__Bacilli             o__Lactobacillales  f__La… g__L… s__un_…
 3 p__Proteobacteria    c__Alphaproteobacteria o__Rhodobacterales  f__Rh… g__P… s__un_…
 4 p__Proteobacteria    c__Gammaproteobacteria o__Aeromonadales    f__Ae… g__A… s__un_…
 5 p__Bacteroidota      c__Bacteroidia         o__Cytophagales     f__Sp… g__A… s__un_…
 6 p__Proteobacteria    c__Gammaproteobacteria o__Burkholderiales  f__Co… g__P… s__un_…
 7 p__Verrucomicrobiota c__Verrucomicrobiae    o__Verrucomicrobia… f__Ru… g__L… s__un_…
 8 p__Proteobacteria    c__Alphaproteobacteria o__Rhodobacterales  f__Rh… g__R… s__un_…
 9 p__Proteobacteria    c__Gammaproteobacteria o__Enterobacterales f__En… g__E… s__un_…
10 p__Proteobacteria    c__Gammaproteobacteria o__Burkholderiales  f__Su… g__A… s__un_…
# … with 286,722 more rows
# ℹ Use `print(n = ...)` to see more rows

mpse.rare %>% 
      mp_plot_rarecurve(
         .rare = Abundance, 
         .alpha = Observe,
      )
Error in `dplyr::select()`:
! Can't subset columns that don't exist.
✖ Column `Abundance` doesn't exist.
Backtrace:
 1. mpse.rare %>% ...
 8. dplyr:::select.data.frame(., !!rlang::sym("Sample"), !!.rare)
 Error in dplyr::select(., !!rlang::sym("Sample"), !!.rare) :
Dominant language
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