Relative abundance barplot

Source: R/abundance_barplot.R

Generates a bar plot of relative abundance (%) for the most abundant taxa groups across samples or sample groups.

abundance_barplot(
  table,
  metadata,
  taxonomy_db = "silva",
  level = "genus",
  x_col,
  facet_col = NULL,
  width_equal = FALSE,
  label = "taxonomy",
  top_n = 15,
  x_axis_title = "Samples",
  add_remained = FALSE,
  save_table = TRUE,
  table_filename = "relative_abundance.txt"
)

Arguments

table

A data frame with taxa in rows and samples in columns. The first column must be named taxonomy, containing full taxonomic strings.

metadata

A data frame containing sample metadata. Must include a SAMPLEID column matching sample names in table.

taxonomy_db

Character. Reference taxonomy database: "silva" (default). Affects how taxonomic names are simplified in the plot.

level

Character. Taxonomic level to collapse: "genus" (default) or "phylum".

x_col

Character. Column name in metadata to use for the x-axis (e.g., environment, condition).

facet_col

Optional. Character. Column name in metadata to facet the plot by (e.g., treatment group). Default is NULL.

label

Character. Legend title for the taxa groups. Default is "taxonomy".

top_n

Integer. Number of most abundant taxa groups to display. Default is 15.

x_axis_title

Character. The tittle that should be in the x-axis (deault = "Samples")

add_remained

Logical indicating whether to include an "Other" category to sum remaining groups; default is FALSE.

Value

A ggplot2 object showing a stacked barplot of relative abundances.

Details

  • Relative abundances are calculated per sample (%).

  • Taxa names are collapsed to the specified taxonomic level ("genus" or "phylum").

  • Only the top top_n taxa are shown; others are filtered out.

  • Samples are grouped and ordered according to x_col.

  • Optional faceting by facet_col if provided.

  • Taxonomic strings matching "d__Bacteria;__;__;__;__;__" are automatically removed.

Examples

abundance_barplot( table = table_taxa,
                             metadata = metadata,
                             taxonomy_db = "silva",
                             level = "genus",
                             x_col = "MUESTRA",
                             label = "Genus",
                             facet_col = "SITIO",
                             width_equal = FALSE,
                             group_var = "SAMPLEID",
                             top_n = 30,
                             add_remained  = TRUE)
#> Error in abundance_barplot(table = table_taxa, metadata = metadata, taxonomy_db = "silva",     level = "genus", x_col = "MUESTRA", label = "Genus", facet_col = "SITIO",     width_equal = FALSE, group_var = "SAMPLEID", top_n = 30,     add_remained = TRUE): unused argument (group_var = "SAMPLEID")