plot_composition {microbiome} | R Documentation

## Taxonomic Composition Plot

### Description

Plot taxon abundance for samples.

### Usage

    plot_composition(
      x,
      sample.sort = NULL,
      otu.sort = NULL,
      x.label = "sample",
      plot.type = "barplot",
      verbose = FALSE,
      average_by = NULL,
      group_by = NULL,
      ...
    )

### Arguments

`x` | `phyloseq-class` object
`sample.sort` | Order samples. Various criteria are available: NULL or 'none': No sorting A single character string: indicate the metadata field to be used for ordering. Or: if this string is found from the tax_table, then sort by the corresponding taxonomic group. A character vector: sample IDs indicating the sample ordering. 'neatmap' Order samples based on the neatmap approach. See `neatsort`. By default, 'NMDS' method with 'bray' distance is used. For other options, arrange the samples manually with the function.
`otu.sort` | Order taxa. Same options as for the sample.sort argument but instead of metadata, taxonomic table is used. Also possible to sort by 'abundance'.
`x.label` | Specify how to label the x axis. This should be one of the variables in sample_variables(x).
`plot.type` | Plot type: 'barplot' or 'heatmap'
`verbose` | verbose (but not in sample/taxon ordering). The options are 'Z-OTU', 'Z-Sample', 'log10' and 'compositional'. See the `transform` function.
`average_by` | Average the samples by the average_by variable
`group_by` | Group by this variable (in plot.type "barplot")
`...` | Arguments to be passed (for `neatsort` function)

### Value

A `ggplot` plot object.

### Examples

    library(dplyr)
    data(atlas1006)
    pseq <- atlas1006 %>%
       subset_samples(DNA_extraction_method == "r") %>%
       aggregate_taxa(level = "Phylum") %>%
       transform(transform = "compositional")
    p <- plot_composition(pseq, sample.sort = "Firmicutes",
             otu.sort = "abundance", verbose = TRUE) +
         scale_fill_manual(values = default_colors("Phylum")[taxa(pseq)])

[Package microbiome version 1.12.0 Index]