Display taxa abundances as a stacked bar graph.

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.

Abbreviations are allowed. Default: "singly"

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.

Details

If biom is rarefied, then relative abundance will be shown on the y-axis. Otherwise, raw abundance will be displayed.

See also

Other taxa_abundance: sample_sums(), taxa_boxplot(), taxa_clusters(), taxa_corrplot(), taxa_heatmap(), taxa_stats(), taxa_sums(), taxa_table()

Other visualization: adiv_boxplot(), adiv_corrplot(), bdiv_boxplot(), bdiv_corrplot(), bdiv_heatmap(), bdiv_ord_plot(), plot_heatmap(), rare_corrplot(), rare_multiplot(), rare_stacked(), stats_boxplot(), stats_corrplot(), taxa_boxplot(), taxa_corrplot(), taxa_heatmap()

Examples

    library(rbiom)
    
    biom <- rarefy(hmp50)
    
    taxa_stacked(biom, rank="Phylum")

    
    taxa_stacked(biom, rank = "genus", facet.by = "body site")