Add taxon prevalences to the taxon table

add_prevalence() calculates taxon prevalences (overall or per condition) and adds it to the taxa table under the column name "prevalence". Prevalence can be expressed as the number of samples where a taxon occurs or the ratio of samples where a taxon occurs and the total amount of samples.

Usage

add_prevalence(ta, condition = NULL, relative = FALSE, fisher_test = FALSE)

Arguments

ta

A tidytacos object.

condition

A categorical variable (string).

relative

Whether to use relative occurrences.

fisher_test

Whether to perform a fisher test and add the p-values of the test to the taxa table.

Value

A tidytacos object.

Details

If 'condition' is specified, the prevalences will be calculated separately for each group defined by the condition variable. This variable should be present in the sample table.

If condition is specified, differential prevalence testing can be performed by setting the fisher_test argument. Options are F (default) or T. When set to T, significance of differential prevalence will be added to the taxa table under column name fisher_p.

Condition should be a categorical variable present in the samples table. Supply condition as a string.

See also

Other taxa-modifiers: add_mean_rel_abundance(), add_taxon_name(), add_taxon_name_color()

Examples

# add prevalences of all taxa
urtp <- urt %>% add_prevalence()
urtp$taxa %>% dplyr::select(taxon_id, prevalence)
#> # A tibble: 1,957 × 2
#>    taxon_id prevalence
#>    <chr>         <int>
#>  1 t1               86
#>  2 t2              207
#>  3 t3                7
#>  4 t4                5
#>  5 t5               16
#>  6 t6               22
#>  7 t7              155
#>  8 t8               25
#>  9 t9               24
#> 10 t10               1
#> # ℹ 1,947 more rows

# add prevalences and fisher test for location
urtpf <- urt %>%
  add_prevalence(condition="location", fisher_test=TRUE, relative=TRUE)
urtpf$taxa %>%
  dplyr::select(taxon_id, prevalence_in_N, prevalence_in_NF, fisher_p)
#> # A tibble: 1,957 × 4
#>    taxon_id prevalence_in_N prevalence_in_NF fisher_p
#>    <chr>              <dbl>            <dbl>    <dbl>
#>  1 t1                0.326           0.443    0.0885 
#>  2 t2                0.988           0.931    0.0437 
#>  3 t3                0.0233          0.0382   0.706  
#>  4 t4                0.0233          0.0229   1      
#>  5 t5                0.0581          0.0840   0.599  
#>  6 t6                0.128           0.0840   0.359  
#>  7 t7                0.814           0.649    0.0120 
#>  8 t8                0.0465          0.160    0.00933
#>  9 t9                0.0349          0.160    0.00354
#> 10 t10               0               0.00763  1      
#> # ℹ 1,947 more rows