Ordinate samples and taxa on a 2D plane based on beta diversity distances.

Ordinate samples and taxa on a 2D plane based on beta diversity distances.

Usage

bdiv_ord_plot(
  biom,
  bdiv = "Bray-Curtis",
  ord = "PCoA",
  weighted = TRUE,
  layers = "petm",
  stat.by = NULL,
  facet.by = NULL,
  colors = TRUE,
  shapes = TRUE,
  tree = NULL,
  test = "adonis2",
  seed = 0,
  permutations = 999,
  rank = -1,
  taxa = 4,
  p.top = Inf,
  p.adj = "fdr",
  unc = "singly",
  caption = TRUE,
  underscores = FALSE,
  ...
)

Arguments

biom

An rbiom object, such as from as_rbiom(). Any value accepted by as_rbiom() can also be given here.

bdiv

Beta diversity distance algorithm(s) to use. Options are: "Bray-Curtis", "Manhattan", "Euclidean", "Jaccard", and "UniFrac". For "UniFrac", a phylogenetic tree must be present in biom or explicitly provided via tree=. Multiple/abbreviated values allowed. Default: "Bray-Curtis"

ord

Method for reducing dimensionality. Options are:

"PCoA" -

Principal coordinate analysis; ape::pcoa().

"UMAP" -

Uniform manifold approximation and projection; uwot::umap().

"NMDS" -

Nonmetric multidimensional scaling; vegan::metaMDS().

"tSNE" -

t-distributed stochastic neighbor embedding; tsne::tsne().

Multiple/abbreviated values allowed. Default: "PCoA"

weighted

Take relative abundances into account. When weighted=FALSE, only presence/absence is considered. Multiple values allowed. Default: TRUE

layers

One or more of c("point", "spider", "ellipse", "name", "mean", "taxon", "arrow"). The first four are sample-centric; the last three are taxa-centric. Single letter abbreviations are also accepted. For instance, c("point", "ellipse") is equivalent to c("p", "e") and "pe". Default: "pe"

stat.by

The categorical or numeric metadata field over which statistics should be calculated. Required.

facet.by

Dataset field(s) to use for faceting. Must be categorical. Default: NULL

colors

How to color the groups. Options are:

TRUE -

Automatically select colorblind-friendly colors.

FALSE or NULL -

Don't use colors.

a palette name -

Auto-select colors from this set. E.g. "okabe"

character vector -

Custom colors to use. E.g. c("red", "#00FF00")

named character vector -

Explicit mapping. E.g. c(Male = "blue", Female = "red")

See "Aesthetics" section below for additional information. Default: TRUE

shapes

Shapes for each group. Options are similar to colors's: TRUE, FALSE, NULL, shape names (typically integers 0 - 17), or a named vector mapping groups to specific shape names. See "Aesthetics" section below for additional information. Default: TRUE

tree

A phylo object representing the phylogenetic relationships of the taxa in biom. Only required when computing UniFrac distances. Default: biom$tree

test

Permutational test for accessing significance. Options are:

"adonis2" -

Permutational MANOVA; vegan::adonis2().

"mrpp" -

Multiple response permutation procedure; vegan::mrpp().

"none" -

Don't run any statistics.

Abbreviations are allowed. Default: "adonis2"

seed

Random seed for permutations. Must be a non-negative integer. Default: 0

permutations

Number of random permutations to use. Default: 999

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.

p.top

Only display taxa with the most significant differences in abundance. If p.top is >= 1, then the p.top most significant taxa are displayed. If p.top is less than one, all taxa with an adjusted p-value <= p.top are displayed. Recommended to be used in combination with the taxa parameter to set a lower bound on the mean abundance of considered taxa. Default: Inf

p.adj

Method to use for multiple comparisons adjustment of p-values. Run p.adjust.methods for a list of available options. Default: "fdr"

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"

caption

Add methodology caption beneath the plot. Default: TRUE

underscores

When parsing the tree, should underscores be kept as is? By default they will be converted to spaces (unless the entire ID is quoted). Default FALSE

...

Parameters for layer geoms (e.g. ggplot2::geom_point()). Prefixing parameter names with a layer name ensures that a particular parameter is passed to, and only to, that layer. For instance, point.size = 2 or p.size = 2 ensures only the points have their size set to 2. Points can also be controlled with the pt. prefix.

Value

A ggplot2 plot. The computed sample coordinates and ggplot command are available as $data and $code respectively. If stat.by is given, then $stats and $stats$code are set. If rank is given, then $data$taxa_coords, $taxa_stats, and $taxa_stats$code are set.

See also

Other beta_diversity: bdiv_boxplot(), bdiv_clusters(), bdiv_corrplot(), bdiv_heatmap(), bdiv_ord_table(), bdiv_stats(), bdiv_table(), distmat_stats()

Other ordination: bdiv_ord_table(), distmat_ord_table()

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

Examples

    library(rbiom)
    
    biom <- rarefy(hmp50)
    
    bdiv_ord_plot(biom, layers="pemt", stat.by="Body Site", rank="g")