Skip to contents

Summarize a tax_table (taxonomic slot of phyloseq object) using gtsummary

Source: R/dada_phyloseq.R
tbl_sum_taxtable.Rd

lifecycle-maturing

Mainly a wrapper for the gtsummary::tbl_summary() function in the case of physeq object.

Usage

tbl_sum_taxtable(physeq, taxonomic_ranks = NULL, ...)

Arguments

physeq

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

taxonomic_ranks

A list of taxonomic ranks we want to summarized.

...

Additional arguments passed on to gtsummary::tbl_summary()

Value

A table of class c('tbl_summary', 'gtsummary')

Author

Adrien Taudière

Examples

tbl_sum_taxtable(data_fungi_mini)



  
Characteristic
      N = 451
    
Domain

    Fungi
45 (100%)
Phylum

    Basidiomycota
45 (100%)
Class

    Agaricomycetes
41 (93%)
    Atractiellomycetes
1 (2.3%)
    Tremellomycetes
2 (4.5%)
    Unknown
1
Order

    Agaricales
7 (17%)
    Atractiellales
1 (2.4%)
    Auriculariales
6 (14%)
    Cantharellales
1 (2.4%)
    Corticiales
1 (2.4%)
    Hymenochaetales
5 (12%)
    Polyporales
11 (26%)
    Russulales
9 (21%)
    Tremellales
1 (2.4%)
    Unknown
3
Family

    Aporpiaceae
1 (2.6%)
    Atractiellales_fam_Incertae_sedis
1 (2.6%)
    Auriculariaceae
2 (5.1%)
    Cantharellales_fam_Incertae_sedis
1 (2.6%)
    Corticiaceae
1 (2.6%)
    Entolomataceae
1 (2.6%)
    Exidiaceae
3 (7.7%)
    Hericiaceae
1 (2.6%)
    Hymenochaetales_fam_Incertae_sedis
1 (2.6%)
    Hyphodermataceae
2 (5.1%)
    Lyophyllaceae
4 (10%)
    Peniophoraceae
1 (2.6%)
    Phanerochaetaceae
1 (2.6%)
    Polyporaceae
5 (13%)
    Pterulaceae
1 (2.6%)
    Russulales_fam_Incertae_sedis
1 (2.6%)
    Schizoporaceae
4 (10%)
    Steccherinaceae
1 (2.6%)
    Stereaceae
6 (15%)
    Tricholomataceae
1 (2.6%)
    Unknown
6
Genus

    Antrodiella
1 (2.7%)
    Auricularia
2 (5.4%)
    Basidiodendron
1 (2.7%)
    Elmerina
1 (2.7%)
    Entocybe
1 (2.7%)
    Exidia
2 (5.4%)
    Fomes
4 (11%)
    Gloeohypochnicium
1 (2.7%)
    Helicogloea
1 (2.7%)
    Hericium
1 (2.7%)
    Hyphoderma
2 (5.4%)
    Marchandiomyces
1 (2.7%)
    Mycena
1 (2.7%)
    Ossicaulis
4 (11%)
    Peniophora
1 (2.7%)
    Peniophorella
1 (2.7%)
    Phanerochaete
1 (2.7%)
    Radulomyces
1 (2.7%)
    Sistotrema
1 (2.7%)
    Stereum
4 (11%)
    Trametes
1 (2.7%)
    Xylodon
4 (11%)
    Unknown
8
Species

    analogum
1 (2.9%)
    brasiliensis
1 (2.9%)
    buckii
1 (2.9%)
    caryae
1 (2.9%)
    coralloides
1 (2.9%)
    eyrei
1 (2.9%)
    flaviporus
1 (2.9%)
    fomentarius
4 (11%)
    glandulosa
2 (5.7%)
    hirsutum
1 (2.9%)
    lachnopus
4 (11%)
    livescens
1 (2.9%)
    mesenterica
1 (2.9%)
    molaris
1 (2.9%)
    oblongisporum
1 (2.9%)
    ostrea
3 (8.6%)
    pellucida
1 (2.9%)
    pubera
1 (2.9%)
    raduloides
3 (8.6%)
    renati
1 (2.9%)
    roseocremeum
1 (2.9%)
    setigerum
1 (2.9%)
    versicolor
1 (2.9%)
    versiformis
1 (2.9%)
    Unknown
10
Trophic.Mode

    -
5 (11%)
    Pathotroph
1 (2.2%)
    Pathotroph-Saprotroph
2 (4.4%)
    Pathotroph-Saprotroph-Symbiotroph
1 (2.2%)
    Saprotroph
33 (73%)
    Saprotroph-Symbiotroph
3 (6.7%)
Guild

    -
5 (11%)
    Ectomycorrhizal-Wood Saprotroph
1 (2.2%)
    Endophyte-Undefined Saprotroph
2 (4.4%)
    Fungal Parasite-Undefined Saprotroph
1 (2.2%)
    Leaf Saprotroph-Plant Pathogen-Undefined Saprotroph-Wood Saprotroph
1 (2.2%)
    Lichen Parasite
1 (2.2%)
    Plant Pathogen-Wood Saprotroph
1 (2.2%)
    Undefined Saprotroph
20 (44%)
    Wood Saprotroph
11 (24%)
    Wood Saprotroph-Undefined Saprotroph
2 (4.4%)
Trait

    -
13 (29%)
    Brown Rot
13 (29%)
    Brown Rot-White Rot
13 (29%)
    White Rot
13 (29%)
Confidence.Ranking

    -
5 (11%)
    Highly Probable
3 (6.7%)
    Possible
2 (4.4%)
    Probable
35 (78%)
Genus_species

    Antrodiella_brasiliensis
1 (2.2%)
    Auricularia_NA
1 (2.2%)
    Auricularia_mesenterica
1 (2.2%)
    Basidiodendron_eyrei
1 (2.2%)
    Elmerina_caryae
1 (2.2%)
    Entocybe_NA
1 (2.2%)
    Exidia_glandulosa
2 (4.4%)
    Fomes_fomentarius
4 (8.9%)
    Gloeohypochnicium_analogum
1 (2.2%)
    Helicogloea_pellucida
1 (2.2%)
    Hericium_coralloides
1 (2.2%)
    Hyphoderma_roseocremeum
1 (2.2%)
    Hyphoderma_setigerum
1 (2.2%)
    Marchandiomyces_buckii
1 (2.2%)
    Mycena_renati
1 (2.2%)
    NA_NA
8 (18%)
    Ossicaulis_lachnopus
4 (8.9%)
    Peniophora_versiformis
1 (2.2%)
    Peniophorella_pubera
1 (2.2%)
    Phanerochaete_livescens
1 (2.2%)
    Radulomyces_molaris
1 (2.2%)
    Sistotrema_oblongisporum
1 (2.2%)
    Stereum_hirsutum
1 (2.2%)
    Stereum_ostrea
3 (6.7%)
    Trametes_versicolor
1 (2.2%)
    Xylodon_flaviporus
1 (2.2%)
    Xylodon_raduloides
3 (6.7%)
1 n (%)
    
data_fungi_mini |>
  filt_taxa_pq(min_occurence = 2) |>
  tbl_sum_taxtable(taxonomic_rank = c("Species", "Genus"))
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 45
#> Number of filtered-out ASV 2
#> Number of kept ASV 43
#> Number of kept samples 137



  
Characteristic
      N = 431
    
Species

    analogum
1 (2.9%)
    brasiliensis
1 (2.9%)
    buckii
1 (2.9%)
    caryae
1 (2.9%)
    coralloides
1 (2.9%)
    eyrei
1 (2.9%)
    flaviporus
1 (2.9%)
    fomentarius
4 (12%)
    glandulosa
1 (2.9%)
    hirsutum
1 (2.9%)
    lachnopus
4 (12%)
    livescens
1 (2.9%)
    mesenterica
1 (2.9%)
    molaris
1 (2.9%)
    oblongisporum
1 (2.9%)
    ostrea
3 (8.8%)
    pellucida
1 (2.9%)
    pubera
1 (2.9%)
    raduloides
3 (8.8%)
    renati
1 (2.9%)
    roseocremeum
1 (2.9%)
    setigerum
1 (2.9%)
    versicolor
1 (2.9%)
    versiformis
1 (2.9%)
    Unknown
9
Genus

    Antrodiella
1 (2.9%)
    Auricularia
1 (2.9%)
    Basidiodendron
1 (2.9%)
    Elmerina
1 (2.9%)
    Entocybe
1 (2.9%)
    Exidia
1 (2.9%)
    Fomes
4 (11%)
    Gloeohypochnicium
1 (2.9%)
    Helicogloea
1 (2.9%)
    Hericium
1 (2.9%)
    Hyphoderma
2 (5.7%)
    Marchandiomyces
1 (2.9%)
    Mycena
1 (2.9%)
    Ossicaulis
4 (11%)
    Peniophora
1 (2.9%)
    Peniophorella
1 (2.9%)
    Phanerochaete
1 (2.9%)
    Radulomyces
1 (2.9%)
    Sistotrema
1 (2.9%)
    Stereum
4 (11%)
    Trametes
1 (2.9%)
    Xylodon
4 (11%)
    Unknown
8
1 n (%)