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Permanova on a phyloseq object

Source: R/beta_div_test.R
adonis_pq.Rd

lifecycle-experimental

A wrapper for the vegan::adonis2() function in the case of physeq object.

Usage

adonis_pq(
  physeq,
  formula,
  dist_method = "bray",
  merge_sample_by = NULL,
  na_remove = FALSE,
  correction_for_sample_size = FALSE,
  rarefy_nb_seqs = FALSE,
  rngseed = FALSE,
  verbose = TRUE,
  ...
)

Arguments

physeq

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

formula

(required) the right part of a formula for vegan::adonis2(). Variables must be present in the physeq@sam_data slot.

dist_method

(default "bray") the distance used. See phyloseq::distance() for all available distances or run phyloseq::distanceMethodList(). For aitchison and robust.aitchison distance, vegan::vegdist() function is directly used.

merge_sample_by

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

na_remove

(logical, default FALSE) If set to TRUE, remove samples with NA in the variables set in formula.

correction_for_sample_size

(logical, default FALSE) If set to TRUE, the sample size (number of sequences by samples) is added to formula in the form y~Library_Size + Biological_Effect following recommendation of Weiss et al. 2017. correction_for_sample_size overcome rarefy_nb_seqs if both are TRUE.

rarefy_nb_seqs

(logical, default FALSE) Rarefy each sample (before merging if merge_sample_by is set) using phyloseq::rarefy_even_depth(). if correction_for_sample_size is TRUE, rarefy_nb_seqs will have no effect.

rngseed

(Optional). A single integer value passed to phyloseq::rarefy_even_depth(), which is used to fix a seed for reproducibly random number generation (in this case, reproducibly random subsampling). If set to FALSE, then no fiddling with the RNG seed is performed, and it is up to the user to appropriately call set.seed beforehand to achieve reproducible results. Default is FALSE.

verbose

(logical, default TRUE) If TRUE, prompt some messages.

...

Additional arguments passed on to vegan::adonis2() function. Note that the parameter by is important. If by is set to NULL (default) the p-value is computed for the entire model. by = NULL will assess the overall significance of all terms together, by = "terms" will assess significance for each term (sequentially from first to last), setting by = "margin" will assess the marginal effects of the terms (each marginal term analyzed in a model with all other variables), by = "onedf" will analyze one-degree-of-freedom contrasts sequentially. The argument is passed on to anova.cca.

Value

The function returns an anova.cca result object with a new column for partial R^2. See help of vegan::adonis2() for more information.

Details

This function is mainly a wrapper of the work of others. Please make a reference to vegan::adonis2() if you use this function.

Author

Adrien Taudière

Examples

data(enterotype)
# \donttest{
adonis_pq(enterotype, "SeqTech*Enterotype", na_remove = TRUE)
#> Taxa are now in columns.
#> SeqTech
#> Enterotype
#> 9 were discarded due to NA in variables present in formula.
#> Permutation test for adonis under reduced model
#> Permutation: free
#> Number of permutations: 999
#> 
#> vegan::adonis2(formula = .formula, data = metadata)
#>           Df SumOfSqs      R2      F Pr(>F)    
#> Model      8   38.194 0.70766 79.278  0.001 ***
#> Residual 262   15.778 0.29234                  
#> Total    270   53.972 1.00000                  
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
adonis_pq(enterotype, "SeqTech*Enterotype", na_remove = TRUE, by = "terms")
#> Taxa are now in columns.
#> SeqTech
#> Enterotype
#> 9 were discarded due to NA in variables present in formula.
#> Permutation test for adonis under reduced model
#> Terms added sequentially (first to last)
#> Permutation: free
#> Number of permutations: 999
#> 
#> vegan::adonis2(formula = .formula, data = metadata, by = "terms")
#>                     Df SumOfSqs      R2        F Pr(>F)    
#> SeqTech              2   29.175 0.54055 242.2289  0.001 ***
#> Enterotype           2    8.651 0.16028  71.8250  0.001 ***
#> SeqTech:Enterotype   4    0.368 0.00683   1.5293  0.112    
#> Residual           262   15.778 0.29234                    
#> Total              270   53.972 1.00000                    
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
adonis_pq(enterotype, "SeqTech*Enterotype", na_remove = TRUE, by = "onedf")
#> Taxa are now in columns.
#> SeqTech
#> Enterotype
#> 9 were discarded due to NA in variables present in formula.
#> Permutation test for adonis under reduced model
#> Sequential test for contrasts
#> Permutation: free
#> Number of permutations: 999
#> 
#> vegan::adonis2(formula = .formula, data = metadata, by = "onedf")
#>                             Df SumOfSqs       R2        F Pr(>F)    
#> SeqTechPyro454               1   28.796  0.53353 478.1659  0.001 ***
#> SeqTechSanger                1    0.379  0.00702   6.2918  0.001 ***
#> Enterotype2                  1    4.282  0.07933  71.1013  0.001 ***
#> Enterotype3                  1    4.369  0.08095  72.5487  0.001 ***
#> SeqTechPyro454:Enterotype2   1   -0.556 -0.01030  -9.2315  1.000    
#> SeqTechSanger:Enterotype2    1    0.232  0.00430   3.8560  0.015 *  
#> SeqTechPyro454:Enterotype3   1    0.443  0.00820   7.3535  0.001 ***
#> SeqTechSanger:Enterotype3    1    0.249  0.00462   4.1394  0.009 ** 
#> Residual                   262   15.778  0.29234                    
#> Total                      270   53.972  1.00000                    
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
adonis_pq(enterotype, "SeqTech*Enterotype", na_remove = TRUE, by = "margin")
#> Taxa are now in columns.
#> SeqTech
#> Enterotype
#> 9 were discarded due to NA in variables present in formula.
#> Permutation test for adonis under reduced model
#> Marginal effects of terms
#> Permutation: free
#> Number of permutations: 999
#> 
#> vegan::adonis2(formula = .formula, data = metadata, by = "margin")
#>                     Df SumOfSqs      R2      F Pr(>F)  
#> SeqTech:Enterotype   4    0.368 0.00683 1.5293  0.092 .
#> Residual           262   15.778 0.29234                
#> Total              270   53.972 1.00000                
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

adonis_pq(enterotype, "SeqTech", dist_method = "jaccard", by = "terms")
#> Taxa are now in columns.
#> Permutation test for adonis under reduced model
#> Terms added sequentially (first to last)
#> Permutation: free
#> Number of permutations: 999
#> 
#> vegan::adonis2(formula = .formula, data = metadata, by = "terms")
#>           Df SumOfSqs      R2      F Pr(>F)    
#> SeqTech    2   31.330 0.40211 93.147  0.001 ***
#> Residual 277   46.585 0.59789                  
#> Total    279   77.915 1.00000                  
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
adonis_pq(enterotype, "SeqTech", dist_method = "robust.aitchison", by = "terms")
#> Taxa are now in columns.
#> Permutation test for adonis under reduced model
#> Terms added sequentially (first to last)
#> Permutation: free
#> Number of permutations: 999
#> 
#> vegan::adonis2(formula = .formula, data = metadata, by = "terms")
#>           Df SumOfSqs      R2    F Pr(>F)    
#> SeqTech    2   121403 0.95598 3008  0.001 ***
#> Residual 277     5590 0.04402                
#> Total    279   126992 1.00000                
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
# }