Write, Analyze, and Visualize 'BIOM' Data

taxa_stacked

R Documentation

Display taxa abundances as a stacked bar graph.

Description

Display taxa abundances as a stacked bar graph.

Usage

taxa_stacked(
  biom,
  rank = -1,
  taxa = 6,
  colors = TRUE,
  patterns = FALSE,
  label.by = NULL,
  order.by = NULL,
  facet.by = NULL,
  dist = "euclidean",
  clust = "complete",
  other = TRUE,
  unc = "singly",
  lineage = FALSE,
  xlab.angle = 90,
  ...
)

Arguments

`biom`	An rbiom object, such as from `as_rbiom()`. Any value accepted by `as_rbiom()` can also be given here.
`rank`	What rank(s) of taxa to display. E.g. `"Phylum"`, `"Genus"`, `".otu"`, etc. An integer vector can also be given, where `1` is the highest rank, `2` is the second highest, `-1` is the lowest rank, `-2` is the second lowest, and `0` is the OTU "rank". Run `biom$ranks` to see all options for a given rbiom object. Default: `-1`.
`taxa`	Which taxa to display. An integer value will show the top n most abundant taxa. A value 0 <= n < 1 will show any taxa with that mean abundance or greater (e.g. `0.1` implies >= 10%). A character vector of taxa names will show only those named taxa. Default: `6`.
`colors`, `patterns`	A character vector of colors or patterns to use in the graph. A named character vector can be used to map taxon names to specific colors or patterns. Set to `TRUE` to auto-select colors or patterns, or to `FALSE` to disable per-taxa colors or patterns. Default: `colors=TRUE, patterns=FALSE`.
`label.by`, `order.by`	What metadata column to use for labeling and/or sorting the samples across the x-axis. Set `label.by='.sample'` to display sample names. When `order.by=NULL`, samples are arranged based on `dist` and `clust`, below. Default: `label.by=NULL, order.by=NULL`.
`facet.by`	Dataset field(s) to use for faceting. Must be categorical. Default: `NULL`
`dist`, `clust`	Distance (`stats::dist()`) and clustering (`stats::hclust()`) methods to use for automatically arranging samples along the x-axis to put samples with similar composition near one another. Default: `dist="euclidean", clust="complete"`.
`other`	Sum all non-itemized taxa into an "Other" taxa. When `FALSE`, only returns taxa matched by the `taxa` argument. Specifying `TRUE` adds "Other" to the returned set. A string can also be given to imply `TRUE`, but with that value as the name to use instead of "Other". Default: `FALSE`
`unc`	How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are: `"singly"` - Replaces them with the OTU name. `"grouped"` - Replaces them with a higher rank's name. `"drop"` - Excludes them from the result. `"asis"` - To not check/modify any taxa names. Default: `"singly"` Abbreviations are allowed.
`lineage`	Include all ranks in the name of the taxa. For instance, setting to `TRUE` will produce `⁠Bacteria; Actinobacteria; Coriobacteriia; Coriobacteriales⁠`. Otherwise the taxa name will simply be `Coriobacteriales`. You want to set this to TRUE when `unc = "asis"` and you have taxa names (such as Incertae_Sedis) that map to multiple higher level ranks. Default: `FALSE`
`xlab.angle`	Angle of the labels at the bottom of the plot. Options are `"auto"`, `'0'`, `'30'`, and `'90'`. Default: `"auto"`.
`...`	Parameters for underlying functions. Prefixing parameter names with a layer name ensures that a particular parameter is passed to, and only to, that layer.

Value

A ggplot2 plot.
The computed data points and ggplot command are available as ⁠$data⁠ and ⁠$code⁠, respectively.

Examples

    library(rbiom)
    
    biom <- rarefy(hmp50)
    
    taxa_stacked(biom, rank="Phylum")
    
    taxa_stacked(biom, rank = "genus", facet.by = "body site")

cmmr/rbiom documentation built on April 28, 2024, 6:38 a.m.