include.lowest = FALSE in mp_filter_taxa seems not work

Open

#86 opened on Mar 30, 2023 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty: 3/5
Estimated time: 1-2 days
Newbie friendliness: 35/100

Issue type: Bug
Clarity: Mostly clear
Activity status: Stale
Tech stack: r
Domain: data

Research direction

Start by inspecting the mp_filter_taxa implementation and comparing the reported calls with the mouse.time.mpse example dataset. Reproduce the include.lowest behavior with a suitable test case, accounting for the exact argument spelling shown in the report; done means TRUE and FALSE produce the intended distinct filtering results.

Written by the indexing model from the issue text.

Description

When I use the mp_filter_taxa function, I found that include.lowest seems not work, which always return the include.lowest=False reuslt. However, when try it using example dataset mouse.time.mpse, it works fine. I could not figure out why but I think this is very important, because many users may not notice this.
My dataset is unpublic, so if you need it to test, welcome to contact me.

> mp_filter_taxa(mp_raw, .abundance = Abundance, min.abun = 1, min.prop = 0.1, iclude.lowest=FALSE)
# A MPSE-tibble (MPSE object) abstraction: 825,086 × 15
# OTU=6763 | Samples=122 | Assays=Abundance | Taxonomy=Kingdom, Phylum, Class, Order, Family, Genus, Species
   OTU    Sample Abundance origin suborigin bioreptype biotype oritype Kingdom     Phylum      Class Order Family Genus Species
   <chr>  <chr>      <int> <chr>  <chr>     <chr>      <chr>   <chr>   <chr>       <chr>       <chr> <chr> <chr>  <chr> <chr>  
 1 OTU_1  JLBX1E         0 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__E… f__Ye… g__S… s__Ser…
 2 OTU_2  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Bu… g__B… s__Par…
 3 OTU_3  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__X… f__Rh… g__u… s__un_…
 4 OTU_4  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__A… o__S… f__Sp… g__S… s__un_…
 5 OTU_5  JLBX1E        11 JL     BX        1          E       JLE     k__Bacteria p__Bactero… c__B… o__F… f__We… g__C… s__Chr…
 6 OTU_6  JLBX1E         0 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__A… o__R… f__Rh… g__P… s__Phy…
 7 OTU_7  JLBX1E         4 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Bu… g__B… s__un_…
 8 OTU_8  JLBX1E        27 JL     BX        1          E       JLE     k__Bacteria p__Actinob… c__A… o__M… f__Mi… g__M… s__un_…
 9 OTU_9  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__X… f__Rh… g__u… s__un_…
10 OTU_10 JLBX1E         2 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Ox… g__C… s__Col…
# ℹ 825,076 more rows
# ℹ Use `print(n = ...)` to see more rows
> 
> mp_filter_taxa(mp_raw, .abundance = Abundance, min.abun = 1, min.prop = 0.1, iclude.lowest=TRUE)
# A MPSE-tibble (MPSE object) abstraction: 825,086 × 15
# OTU=6763 | Samples=122 | Assays=Abundance | Taxonomy=Kingdom, Phylum, Class, Order, Family, Genus, Species
   OTU    Sample Abundance origin suborigin bioreptype biotype oritype Kingdom     Phylum      Class Order Family Genus Species
   <chr>  <chr>      <int> <chr>  <chr>     <chr>      <chr>   <chr>   <chr>       <chr>       <chr> <chr> <chr>  <chr> <chr>  
 1 OTU_1  JLBX1E         0 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__E… f__Ye… g__S… s__Ser…
 2 OTU_2  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Bu… g__B… s__Par…
 3 OTU_3  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__X… f__Rh… g__u… s__un_…
 4 OTU_4  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__A… o__S… f__Sp… g__S… s__un_…
 5 OTU_5  JLBX1E        11 JL     BX        1          E       JLE     k__Bacteria p__Bactero… c__B… o__F… f__We… g__C… s__Chr…
 6 OTU_6  JLBX1E         0 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__A… o__R… f__Rh… g__P… s__Phy…
 7 OTU_7  JLBX1E         4 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Bu… g__B… s__un_…
 8 OTU_8  JLBX1E        27 JL     BX        1          E       JLE     k__Bacteria p__Actinob… c__A… o__M… f__Mi… g__M… s__un_…
 9 OTU_9  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__X… f__Rh… g__u… s__un_…
10 OTU_10 JLBX1E         2 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Ox… g__C… s__Col…
# ℹ 825,076 more rows
# ℹ Use `print(n = ...)` to see more rows
> mp_filter_taxa(mp_raw, .abundance = Abundance, min.abun = 2, min.prop = 0.1, iclude.lowest=TRUE)
# A MPSE-tibble (MPSE object) abstraction: 545,462 × 15
# OTU=4471 | Samples=122 | Assays=Abundance | Taxonomy=Kingdom, Phylum, Class, Order, Family, Genus, Species
   OTU    Sample Abundance origin suborigin bioreptype biotype oritype Kingdom     Phylum      Class Order Family Genus Species
   <chr>  <chr>      <int> <chr>  <chr>     <chr>      <chr>   <chr>   <chr>       <chr>       <chr> <chr> <chr>  <chr> <chr>  
 1 OTU_1  JLBX1E         0 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__E… f__Ye… g__S… s__Ser…
 2 OTU_2  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Bu… g__B… s__Par…
 3 OTU_3  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__X… f__Rh… g__u… s__un_…
 4 OTU_4  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__A… o__S… f__Sp… g__S… s__un_…
 5 OTU_5  JLBX1E        11 JL     BX        1          E       JLE     k__Bacteria p__Bactero… c__B… o__F… f__We… g__C… s__Chr…
 6 OTU_6  JLBX1E         0 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__A… o__R… f__Rh… g__P… s__Phy…
 7 OTU_7  JLBX1E         4 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Bu… g__B… s__un_…
 8 OTU_8  JLBX1E        27 JL     BX        1          E       JLE     k__Bacteria p__Actinob… c__A… o__M… f__Mi… g__M… s__un_…
 9 OTU_9  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__X… f__Rh… g__u… s__un_…
10 OTU_10 JLBX1E         2 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Ox… g__C… s__Col…
# ℹ 545,452 more rows
# ℹ Use `print(n = ...)` to see more rows
> mp_filter_taxa(mp_raw, .abundance = Abundance, min.abun = 2, min.prop = 0.1, iclude.lowest=FALSE)
# A MPSE-tibble (MPSE object) abstraction: 545,462 × 15
# OTU=4471 | Samples=122 | Assays=Abundance | Taxonomy=Kingdom, Phylum, Class, Order, Family, Genus, Species
   OTU    Sample Abundance origin suborigin bioreptype biotype oritype Kingdom     Phylum      Class Order Family Genus Species
   <chr>  <chr>      <int> <chr>  <chr>     <chr>      <chr>   <chr>   <chr>       <chr>       <chr> <chr> <chr>  <chr> <chr>  
 1 OTU_1  JLBX1E         0 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__E… f__Ye… g__S… s__Ser…
 2 OTU_2  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Bu… g__B… s__Par…
 3 OTU_3  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__X… f__Rh… g__u… s__un_…
 4 OTU_4  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__A… o__S… f__Sp… g__S… s__un_…
 5 OTU_5  JLBX1E        11 JL     BX        1          E       JLE     k__Bacteria p__Bactero… c__B… o__F… f__We… g__C… s__Chr…
 6 OTU_6  JLBX1E         0 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__A… o__R… f__Rh… g__P… s__Phy…
 7 OTU_7  JLBX1E         4 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Bu… g__B… s__un_…
 8 OTU_8  JLBX1E        27 JL     BX        1          E       JLE     k__Bacteria p__Actinob… c__A… o__M… f__Mi… g__M… s__un_…
 9 OTU_9  JLBX1E         1 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__X… f__Rh… g__u… s__un_…
10 OTU_10 JLBX1E         2 JL     BX        1          E       JLE     k__Bacteria p__Proteob… c__G… o__B… f__Ox… g__C… s__Col…
# ℹ 545,452 more rows
# ℹ Use `print(n = ...)` to see more rows

Dominant language: R
Stars: 195
Forks: 36
PR merge metrics: No merged PRs in 30d

Getting set up

This project ships no dev container, Dockerfile or contributing guide, so setting up is up to you: start from its README, and see our first-contribution guide for the general steps.

First steps

Read the whole issue, then the project's contributing guide.
Comment on the issue to say you are picking it up — it saves two people doing the same work.
Fork the repository and make your change on a branch.
Open a pull request that references the issue number.

Similar issues

[R][Parquet] ParquetReaderProperties does not expose page_checksum_verification, so a corrupt page CRC reads silently
Open
- Is something wrong?
Component: R

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

apache/arrow#53138 · Opened Oct 10, 2026

Maintainers usually reply within 1 day
pixi-build-r: recommended packages (MASS, Matrix, mgcv, …) aren't added as dependencies, but conda-forge's r-base doesn't include them
Open
- Is something wrong?
bug pixi-build-r

Difficulty 2/5 1-3 hours Newbie friendliness 70/100

prefix-dev/pixi#7229 · Opened Oct 10, 2026

Maintainers usually reply within 1 day
Incomplete Installation of LaTeX Packages for Language "de-CH"
Open
- Is something wrong?
Difficulty 2/5 1-3 hours Newbie friendliness 78/100

rstudio/tinytex#515 · Opened Oct 10, 2026
Remove needless? dependency on png
Open
- Is something wrong?
Difficulty 2/5 1-3 hours Newbie friendliness 72/100

rstudio/reticulate#1933 · Opened Oct 9, 2026
Set `cli.num_colors = 256^3` when highlighting examples
Open
- Is something wrong?
Difficulty 1/5 Under an hour Newbie friendliness 62/100

r-lib/pkgdown#3028 · Opened Oct 9, 2026

More R issues

include.lowest = FALSE in mp_filter_taxa seems not work

Is something wrong?

Assessment

Research direction

Description

Getting set up

First steps

More from YuLab-SMU/MicrobiotaProcess

Is something wrong?

Is something wrong?

Is something wrong?

Is something wrong?

Is something wrong?

Similar issues

Is something wrong?

Is something wrong?

Is something wrong?

Is something wrong?

Is something wrong?

Get new issues in your inbox