Ordinate samples and taxa on a 2D plane based on beta diversity distances.
Source:R/bdiv_ord_plot.r
bdiv_ord_plot.Rd
Ordinate samples and taxa on a 2D plane based on beta diversity distances.
Usage
bdiv_ord_plot(
biom,
bdiv = "Bray-Curtis",
ord = "UMAP",
weighted = TRUE,
layers = "petm",
stat.by = NULL,
color.by = stat.by,
shape.by = stat.by,
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,
...
)
Arguments
- biom
An rbiom object, such as from
as_rbiom()
. Any value accepted byas_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 inbiom
or explicitly provided viatree=
. Default:"Bray-Curtis"
Multiple/abbreviated values allowed.- ord
Method for reducing dimensionality. Options are:
"UMAP"
- Uniform manifold approximation and projection;uwot::umap()
."PCoA"
- Principal coordinate analysis;ape::pcoa()
."NMDS"
- Nonmetric multidimensional scaling;vegan::metaMDS()
."tSNE"
- t-distributed stochastic neighbor embedding;tsne::tsne()
.
Default:
"UMAP"
Multiple/abbreviated values allowed.- weighted
Take relative abundances into account. When
weighted=FALSE
, only presence/absence is considered. Default:TRUE
Multiple values allowed.- 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 toc("p", "e")
and"pe"
. See plot types for examples of each. Default:"pe"
- stat.by
The categorical or numeric metadata field over which statistics should be calculated. Required.
- color.by, shape.by, facet.by, limit.by
Metadata columns to use for aesthetics and partitioning. See below for details. Default:
NULL
- colors
How to color the groups. Options are:
TRUE
- Automatically select colorblind-friendly colors.FALSE
orNULL
- 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 inbiom
. Only required when computing UniFrac distances. Default:biom$tree
- test
Permutational test for accessing significance. Options are:
"adonis2"
- Permutational MANOVA;vegan::adonis2()
."mrpp"
- Multiple response permutation procedure;vegan::mrpp()
."none"
- Don't run any statistics.
Default:
"adonis2"
Abbreviations are allowed.- seed
Random seed for permutations. Default:
0
- permutations
Number of random permutations to use. Default:
999
- rank
What rank(s) of taxa to display. E.g.
"Phylum"
,"Genus"
,".otu"
, etc. An integer vector can also be given, where1
is the highest rank,2
is the second highest,-1
is the lowest rank,-2
is the second lowest, and0
is the OTU "rank". Runbiom$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 thep.top
most significant taxa are displayed. Ifp.top
is less than one, all taxa with an adjusted p-value <=p.top
are displayed. Recommended to be used in combination with thetaxa
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.
Default:
"singly"
Abbreviations are allowed.- caption
Add methodology caption beneath the plot. Default:
TRUE
- ...
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
orp.size = 2
ensures only the points have their size set to2
. Points can also be controlled with thept.
prefix.
Value
A ggplot2
plot.
The computed sample coordinates and ggplot command
are available as $data
and $code
respectively.
If color.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_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()