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Contingency table of two taxonomic ranks

Source: R/tc_df_pq.R
tc_df_pq.Rd

lifecycle-experimental

Creates a cross-tabulation (contingency table) comparing two taxonomic ranks from a phyloseq object. Useful for comparing taxonomic assignments from different databases, algorithms, or taxonomic levels.

Usage

tc_df_pq(physeq, rank_1 = "Family", rank_2 = "Class", ...)

Arguments

physeq

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

rank_1

(character, default "Family") The name of the first taxonomic rank (column in tax_table slot) for the cross-tabulation rows.

rank_2

(character, default "Class") The name of the second taxonomic rank (column in tax_table slot) for the cross-tabulation columns.

...

Additional arguments passed to gtsummary::tbl_cross().

Value

A gtsummary tbl_cross object displaying the cross-tabulation of the two taxonomic ranks.

Author

Adrien Taudière

Examples

tc_df_pq(data_fungi_mini)



  

      
        
Class

      		
      Total
    
Agaricomycetes
      Atractiellomycetes
      Tremellomycetes
      Unknown
    
Family









    Aporpiaceae
1
0
0
0
1
    Atractiellales_fam_Incertae_sedis
0
1
0
0
1
    Auriculariaceae
2
0
0
0
2
    Cantharellales_fam_Incertae_sedis
1
0
0
0
1
    Corticiaceae
1
0
0
0
1
    Entolomataceae
1
0
0
0
1
    Exidiaceae
3
0
0
0
3
    Hericiaceae
1
0
0
0
1
    Hymenochaetales_fam_Incertae_sedis
1
0
0
0
1
    Hyphodermataceae
2
0
0
0
2
    Lyophyllaceae
4
0
0
0
4
    Peniophoraceae
1
0
0
0
1
    Phanerochaetaceae
1
0
0
0
1
    Polyporaceae
5
0
0
0
5
    Pterulaceae
1
0
0
0
1
    Russulales_fam_Incertae_sedis
1
0
0
0
1
    Schizoporaceae
4
0
0
0
4
    Steccherinaceae
1
0
0
0
1
    Stereaceae
6
0
0
0
6
    Tricholomataceae
1
0
0
0
1
    Unknown
3
0
2
1
6
Total
41
1
2
1
45
tc_df_pq(data_fungi_mini, rank_1 = "Order", rank_2 = "Family")



  

      
        
Family

      		
      Total
    
Aporpiaceae
      Atractiellales_fam_Incertae_sedis
      Auriculariaceae
      Cantharellales_fam_Incertae_sedis
      Corticiaceae
      Entolomataceae
      Exidiaceae
      Hericiaceae
      Hymenochaetales_fam_Incertae_sedis
      Hyphodermataceae
      Lyophyllaceae
      Peniophoraceae
      Phanerochaetaceae
      Polyporaceae
      Pterulaceae
      Russulales_fam_Incertae_sedis
      Schizoporaceae
      Steccherinaceae
      Stereaceae
      Tricholomataceae
      Unknown
    
Order











































    Agaricales
0
0
0
0
0
1
0
0
0
0
4
0
0
0
1
0
0
0
0
1
0
7
    Atractiellales
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
    Auriculariales
1
0
2
0
0
0
3
0
0
0
0
0
0
0
0
0
0
0
0
0
0
6
    Cantharellales
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
    Corticiales
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
    Hymenochaetales
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
4
0
0
0
0
5
    Polyporales
0
0
0
0
0
0
0
0
0
2
0
0
1
5
0
0
0
1
0
0
2
11
    Russulales
0
0
0
0
0
0
0
1
0
0
0
1
0
0
0
1
0
0
6
0
0
9
    Tremellales
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
1
    Unknown
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
3
3
Total
1
1
2
1
1
1
3
1
1
2
4
1
1
5
1
1
4
1
6
1
6
45

if (FALSE) { # \dontrun{
# Compare taxonomic assignments from different methods
ref_fasta <- system.file("extdata", "mini_UNITE_fungi.fasta.gz",
  package = "MiscMetabar", mustWork = TRUE
)
data_fungi_mini2 <- data_fungi_mini |>
  add_new_taxonomy_pq(ref_fasta, suffix = "_sintax", method = "sintax") |>
  add_new_taxonomy_pq(ref_fasta, suffix = "_lca", method = "lca")

tc_df_pq(data_fungi_mini2, rank_1 = "Class_lca", rank_2 = "Class_sintax")
} # }