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Create Barplots for Relative and Absolute Abundance

Source: R/barplot.R
barplot.Rd

This function generates barplots for microbial data at the genus level. It supports both relative and absolute abundance data and can include facets based on available metadata factors. The resulting plots can be saved as PDF files, and the underlying data can be exported as CSV and RDS files.

Usage

barplot(
  physeq = rarefied_genus_psmelt,
  ntaxa = NULL,
  norm_method = NULL,
  sample_matrix = NULL,
  group_by_factor = NULL,
  taxrank = c("Phylum", "Class", "Order", "Family", "Genus"),
  date_factor = NULL
)

Arguments

physeq

A phyloseq object containing the microbiome data. This is the input object that the function processes.

ntaxa

An integer specifying the maximum number of taxa to display in the barplot. Default is 23.

norm_method

A string indicating the normalization method used for absolute abundance data. Options are "fcm" (flow cytometry) or "qpcr" (quantitative PCR). (relative abundance only).

sample_matrix

An optional matrix specifying the sample structure or metadata.

group_by_factor

with this option you can separtate de barplot for factors

taxrank

A character vector indicating the taxonomic levels at which to group the data.

Value

The function generates and saves barplots as PDF files in the project’s figures/ folder. It also saves the processed data as CSV and RDS files in the corresponding output_data/ folders. Additionally, the function outputs the plot object for further customization if needed.

Details

  • Relative abundance plots show proportions of taxa in each sample, with taxa having a mean relative abundance below 1% grouped as "Other".

  • Absolute abundance plots use normalized cell equivalents (norm_method = "fcm" or "qpcr") to display the number of cells per mL for each taxon.

  • Facets are added based on metadata factors present in the phyloseq object.

  • Taxa labels are styled to include genus and species names, if available.

Examples

# Example usage
barplot(
  physeq = rarefied_genus_psmelt,
  ntaxa = 20,
  colorset = my_colors,
  norm_method = "fcm",
  sample_matrix = sample_metadata
)
#> Error in barplot(physeq = rarefied_genus_psmelt, ntaxa = 20, colorset = my_colors,     norm_method = "fcm", sample_matrix = sample_metadata): unused argument (colorset = my_colors)