plot_composition: Taxonomic Composition Plot

In microbiome: Microbiome Analytics

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)]) 

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.