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Compare samples in pairs using diversity and number of ASV including shared ASV.

Source: R/table_functions.R
compare_pairs_pq.Rd

lifecycle-experimental

For the moment refseq slot need to be not Null.

Usage

compare_pairs_pq(
  physeq = NULL,
  bifactor = NULL,
  modality = NULL,
  merge_sample_by = NULL,
  nb_min_seq = 0,
  veg_index = "shannon",
  na_remove = TRUE,
  ...
)

Arguments

physeq

(required) a phyloseq-class object obtained using the phyloseq package.

bifactor

(required) a factor (present in the sam_data slot of the physeq object) presenting the pair names

modality

the name of the column in the sam_data slot of the physeq object to split samples by pairs

merge_sample_by

a vector to determine which samples to merge using the merge_samples2() function. Need to be in physeq@sam_data

nb_min_seq

minimum number of sequences per sample to count the ASV/OTU

veg_index

(default: "shannon") diversity index. "shannon" and "simpson" are computed via divent; other names are forwarded to vegan::diversity().

na_remove

(logical, default TRUE) If set to TRUE, remove samples with NA in the variables set in bifactor, modality and merge_sample_by. NA in variables are well managed even if na_remove = FALSE, so na_remove may be useless.

...

Additional arguments passed to divent::ent_shannon() or divent::ent_simpson() when veg_index is "shannon" or "simpson".

Value

A tibble with information about the number of shared ASV, shared number of sequences and diversity

Examples

data_fungi_mini_lh <- subset_samples(data_fungi_mini, Height %in% c("Low", "High"))
compare_pairs_pq(data_fungi_mini_lh, bifactor = "Height", merge_sample_by = "Height")
#> Taxa are now in columns.
#> Cleaning suppress 5 taxa and 0 samples.
#> # A tibble: 1 × 13
#>   modality nb_ASV_High nb_ASV_Low nb_shared_ASV div_High div_Low nb_shared_seq
#>   <chr>          <dbl>      <dbl>         <dbl>    <dbl>   <dbl>         <dbl>
#> 1 Height            34         34            28     2.56    2.54        151756
#> # ℹ 6 more variables: percent_shared_seq_High <dbl>,
#> #   percent_shared_seq_Low <dbl>, percent_shared_ASV_High <dbl>,
#> #   percent_shared_ASV_Low <dbl>, ratio_nb_High_Low <dbl>,
#> #   ratio_div_High_Low <dbl>
compare_pairs_pq(data_fungi_mini_lh,
  bifactor = "Height",
  merge_sample_by = "Height", modality = "Time"
)
#> Taxa are now in columns.
#> 7 samples were discarded due to NA in variable modality.
#> Cleaning suppress 5 taxa and 0 samples.
#> # A tibble: 4 × 13
#>   modality nb_ASV_High nb_ASV_Low nb_shared_ASV div_High div_Low nb_shared_seq
#>   <chr>          <dbl>      <dbl>         <dbl>    <dbl>   <dbl>         <dbl>
#> 1 0                 13         17             9     1.6     0.74         22914
#> 2 5                 16         20             7     2.1     1.93         15648
#> 3 10                11         13             8     1.34    1.27         11519
#> 4 15                15         16            10     1.68    1.49         60059
#> # ℹ 6 more variables: percent_shared_seq_High <dbl>,
#> #   percent_shared_seq_Low <dbl>, percent_shared_ASV_High <dbl>,
#> #   percent_shared_ASV_Low <dbl>, ratio_nb_High_Low <dbl>,
#> #   ratio_div_High_Low <dbl>