Display shared sample_data modalities — shared_mod

Create a table showing which sample_data variable modalities are shared across phyloseq objects in a list_phyloseq.

Usage

shared_mod_lpq(x, max_modalities = NULL)

shared_mod_lpq(x, max_modalities = NULL)

Arguments

x: (required) A list_phyloseq object.
max_modalities: (integer, default 10) Maximum number of modalities to display per variable.

Value

A tibble or NULL if no shared modalities exist

Details

Examples

# Subset to the 80 most abundant taxa to keep the example fast
# (the full data_fungi has 1420 taxa).
data_fungi_small <- prune_taxa(
  names(sort(taxa_sums(data_fungi), decreasing = TRUE))[1:80],
  data_fungi
)
data_fungi_small <- clean_pq(prune_samples(
  sample_sums(data_fungi_small) >= 500, data_fungi_small
))
lpq <- list_phyloseq(list(data1 = data_fungi_small, data2 = data_fungi_mini))
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: EXPLORATION
#> ℹ 118 common samples, 43 common taxa
#> ✔ list_phyloseq created (EXPLORATION)

shared_mod_lpq(lpq)
#> # A tibble: 5 × 3
#>   Variable     N_shared Shared_modalities                                       
#>   <chr>           <int> <chr>                                                   
#> 1 X                 118 A10-005-B_S188_MERGED.fastq.gz, A10-005-H_S189_MERGED.f…
#> 2 Sample_names      118 A10-005-B_S188, A10-005-H_S189, A10-005-M_S190, A12-007…
#> 3 Tree_name          88 A10-005, A12-007, A8-005, AB29-abm-X, AC27-013, AC29-03…
#> 4 Height              4 Low, High, Middle, NA                                   
#> 5 Diameter           62 52, 28,4, 32,8, 99, 32, 55,4, 115,5, -, 10, 21,5, 40,3,…
shared_mod_lpq(lpq, 10)
#> # A tibble: 5 × 3
#>   Variable     N_shared Shared_modalities                                       
#>   <chr>           <int> <chr>                                                   
#> 1 X                 118 A10-005-B_S188_MERGED.fastq.gz, A10-005-H_S189_MERGED.f…
#> 2 Sample_names      118 A10-005-B_S188, A10-005-H_S189, A10-005-M_S190, A12-007…
#> 3 Tree_name          88 A10-005, A12-007, A8-005, AB29-abm-X, AC27-013, AC29-03…
#> 4 Height              4 Low, High, Middle, NA                                   
#> 5 Diameter           62 52, 28,4, 32,8, 99, 32, 55,4, 115,5, -, 10, 21,5, ... (…
lpq <- list_phyloseq(list(data1 = data_fungi, data2 = data_fungi_mini))
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: NESTED_ROBUSTNESS
#> ℹ 137 common samples, 45 common taxa
#> ✔ list_phyloseq created (NESTED_ROBUSTNESS)

shared_mod_lpq(lpq)
#> # A tibble: 5 × 3
#>   Variable     N_shared Shared_modalities                                       
#>   <chr>           <int> <chr>                                                   
#> 1 X                 137 A10-005-B_S188_MERGED.fastq.gz, A10-005-H_S189_MERGED.f…
#> 2 Sample_names      137 A10-005-B_S188, A10-005-H_S189, A10-005-M_S190, A12-007…
#> 3 Tree_name         100 A10-005, A12-007, A15-004, A8-005, AB29-abm-X, AC27-013…
#> 4 Height              4 Low, High, Middle, NA                                   
#> 5 Diameter           70 52, 28,4, 30,7, 32,8, 33,3, 99, 32, 55,4, 115,5, -, 10,…
shared_mod_lpq(lpq, 10)
#> # A tibble: 5 × 3
#>   Variable     N_shared Shared_modalities                                       
#>   <chr>           <int> <chr>                                                   
#> 1 X                 137 A10-005-B_S188_MERGED.fastq.gz, A10-005-H_S189_MERGED.f…
#> 2 Sample_names      137 A10-005-B_S188, A10-005-H_S189, A10-005-M_S190, A12-007…
#> 3 Tree_name         100 A10-005, A12-007, A15-004, A8-005, AB29-abm-X, AC27-013…
#> 4 Height              4 Low, High, Middle, NA                                   
#> 5 Diameter           70 52, 28,4, 30,7, 32,8, 33,3, 99, 32, 55,4, 115,5, -, ...…