plot_taxa_composition: Taxonomic Composition Plot

In microsud/microbiomeutilities-shiny: microbiomeutilities: An R package with utility functions for the microbiome R package

Description

Plot taxon abundance for samples.

Usage

plot_taxa_composition(x, sample.sort = NULL, taxonomic.level, transform,
  otu.sort = NULL, palette = brewer.pal(12, "Paired"), x.label = "sample",
  plot.type = "barplot", average_by, verbose = FALSE, mar = c(5, 12, 1,
  1), ...)

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 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.
taxonomic.level	Merge the OTUs (for phyloseq object) into a higher taxonomic level. This has to be one from colnames(tax_table(x)).
transform	Data transform to be used in plotting (but not in sample/taxon ordering). The options are 'Z-OTU', 'Z-Sample', 'log10' and 'compositional'. See the transform 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'.
palette	brewer.pal(12, "Paired") the number and palette has to be specified RColorBrewer
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 'lineplot'
average_by	Variable to group.
verbose	verbose
mar	Figure margins
...	Arguments to be passed (for neatsort function)

Value

A ggplot plot object.

Examples

## Not run: 
    # Example data
    library(microbiome)
    library(microbiomeutilities)
    data("biogeogut")
    pseq <- biogeogut
    plot_taxa_composition(pseq, taxonomic.level = "Phylum")
          
## End(Not run)

microsud/microbiomeutilities-shiny documentation built on May 7, 2019, 9:38 a.m.