The subset_ord_plot function is a “convenience function” intended to make it easier to retrieve a plot-derived data.frame with a subset of points according to a threshold and method. The meaning of the threshold depends upon the method.

Load the necessary packages and data.

library("phyloseq"); packageVersion("phyloseq")

## [1] '1.22.3'

library("ggplot2"); packageVersion("ggplot2")

## [1] '2.2.1'

data(GlobalPatterns)

ggplot2 package theme set. See the ggplot2 online documentation for further help.

theme_set(theme_bw())

Some subsetting and light massaging of the GlobalPatterns dataset.

Clean zeros.

GP <- GlobalPatterns
GP <- prune_species(taxa_sums(GP)>0, GP)

## Warning: 'prune_species' is deprecated.
## Use 'prune_taxa' instead.
## See help("Deprecated") and help("phyloseq-deprecated").

Add "human" variable to GP to indicate human-associated samples.

sample_data(GP)$human <- get_variable(GP, "SampleType") %in% c("Feces", "Mock", "Skin", "Tongue")

Subset to just Bacteroidetes phylum.

GP <- subset_taxa(GP, Phylum=="Bacteroidetes")

Perform a correspondence analysis and then create some plots to demonstrate using subset_ord_plot. We want to make species topo with a subset of points layered. Start by performing the correspondence analysis.

gpca <- ordinate(GP, "CCA")

Now make a basic plot of just the species points in the correspondence analysis.

p1 = plot_ordination(GP, gpca, "species", color="Class")
p1

Re-draw this as topo without points, and facet

p0 = ggplot(p1$data, p1$mapping) + geom_density2d() + facet_wrap(~Class)
p0

Re-draw this but include points

p1 = p1 + geom_density2d() + facet_wrap(~Class)
p1

Add a layer of a subset of species-points that are furthest from origin.

p0 + geom_point(data=subset_ord_plot(p1, 0.7, "square"), size=1)

## Warning: Removed 8 rows containing missing values (geom_point).

p0 + geom_point(data=subset_ord_plot(p1, 0.7, "farthest"), size=1)

## Warning: Removed 6 rows containing missing values (geom_point).

p0 + geom_point(data=subset_ord_plot(p1, 0.7, "radial"), size=1)

## Warning: Removed 8 rows containing missing values (geom_point).

Here is what the data retreived by subset_ord_plot actually looks like

head(subset_ord_plot(p1, 0.7, "radial"))

##              CA1      CA2  Kingdom        Phylum           Class
## 554668 1.5118124 1.008842 Bacteria Bacteroidetes Sphingobacteria
## 154451 1.5385689 1.080271 Bacteria Bacteroidetes Sphingobacteria
## 244965 0.9385059 0.364721 Bacteria Bacteroidetes Sphingobacteria
## 62487  1.5268418 1.044843 Bacteria Bacteroidetes Sphingobacteria
## 139513 1.5244189 1.037502 Bacteria Bacteroidetes Sphingobacteria
## 330672 0.8197026 0.149123 Bacteria Bacteroidetes Sphingobacteria
##                     Order       Family    Genus             Species
## 554668 Sphingobacteriales Balneolaceae Balneola                <NA>
## 154451 Sphingobacteriales Balneolaceae Balneola Balneolaalkaliphila
## 244965 Sphingobacteriales Balneolaceae Balneola Balneolaalkaliphila
## 62487  Sphingobacteriales Balneolaceae Balneola                <NA>
## 139513 Sphingobacteriales Balneolaceae Balneola                <NA>
## 330672 Sphingobacteriales Balneolaceae     <NA>                <NA>