Run ANCOMBC2 on phyloseq object — ancombc

A wrapper for the ANCOMBC::ancombc2() function

Usage

ancombc_pq(physeq, fact, levels_fact = NULL, tax_level = "Class", ...)

Arguments

physeq: (required): a phyloseq-class object obtained using the phyloseq package.
fact: (required) Name of the factor in physeq@sam_data used to plot different lines
levels_fact: (default NULL) The order of the level in the factor. Used for reorder levels and select levels (filter out levels not present en levels_fact)
tax_level: The taxonomic level passed on to ANCOMBC::ancombc2()
...: Other arguments passed on to ANCOMBC::ancombc2() function.

Value

The result of ANCOMBC::ancombc2() function

Details

This function is mainly a wrapper of the work of others. Please make a reference to ANCOMBC::ancombc2() if you use this function.

Author

Adrien Taudière

Examples

# \donttest{
if (requireNamespace("mia")) {
  data_fungi_mini@tax_table <- phyloseq::tax_table(cbind(
    data_fungi_mini@tax_table,
    "taxon" = taxa_names(data_fungi_mini)
  ))
  res_height <- ancombc_pq(
    data_fungi_mini,
    fact = "Height",
    levels_fact = c("Low", "High"),
    verbose = TRUE
  )

  ggplot(
    res_height$res,
    aes(
      y = reorder(taxon, lfc_HeightHigh),
      x = lfc_HeightHigh,
      color = diff_HeightHigh
    )
  ) +
    geom_vline(xintercept = 0) +
    geom_segment(aes(
      xend = 0, y = reorder(taxon, lfc_HeightHigh),
      yend = reorder(taxon, lfc_HeightHigh)
    ), color = "darkgrey") +
    geom_point()

  res_time <- ancombc_pq(
    data_fungi_mini,
    fact = "Time",
    levels_fact = c("0", "15"),
    tax_level = "Family",
    verbose = TRUE
  )
}
#> Warning: The group variable has < 3 categories 
#> The multi-group comparisons (global/pairwise/dunnet/trend) will be deactivated
#> Warning: The number of taxa used for estimating sample-specific biases is: 11
#> A large number of taxa (>50) is required for the consistent estimation of biases
#> Obtaining initial estimates ...
#> Estimating sample-specific biases ...
#> Loading required package: foreach
#> 
#> Attaching package: ‘foreach’
#> The following objects are masked from ‘package:purrr’:
#> 
#>     accumulate, when
#> Loading required package: rngtools
#> Warning: Estimation of sampling fractions failed for the following samples:
#> B18-006-B_S19_MERGED.fastq.gz, DY5-004-B_S96_MERGED.fastq.gz, W26-001-B_S165_MERGED.fastq.gz, X24-009-B_S170_MERGED.fastq.gz, X29-004-B_S174_MERGED.fastq.gz, Y28-002-B_S178_MERGED.fastq.gz, Z29-001-H_S185_MERGED.fastq.gz
#> These samples may have an excessive number of zero values
#> Sensitivity analysis for pseudo-count addition to 0s: ...
#> ANCOM-BC2 primary results ...
#> Warning: The group variable has < 3 categories 
#> The multi-group comparisons (global/pairwise/dunnet/trend) will be deactivated
#> Warning: The number of taxa used for estimating sample-specific biases is: 9
#> A large number of taxa (>50) is required for the consistent estimation of biases
#> Obtaining initial estimates ...
#> Estimating sample-specific biases ...
#> Warning: Estimation of sampling fractions failed for the following samples:
#> BT-006-M_S55_MERGED.fastq.gz, C21-NV1-B_S62_MERGED.fastq.gz, CB8-019-H_S70_MERGED.fastq.gz, DY5-004-B_S96_MERGED.fastq.gz, DY5-004-H_S97_MERGED.fastq.gz, J18-004-M_S116_MERGED.fastq.gz, W26-001-B_S165_MERGED.fastq.gz, X24-009-B_S170_MERGED.fastq.gz
#> These samples may have an excessive number of zero values
#> Sensitivity analysis for pseudo-count addition to 0s: ...
#> ANCOM-BC2 primary results ...
# }