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Plot PCoA ordination coordinates from a batch audit

Source: R/plot-ordination.R
plot_ordination.Rd

plot_ordination() visualizes the first two PCoA axes stored by check_batch(). Points can be colored by any audited outcome, batch, or covariate variable stored with the ordination coordinates.

Usage

plot_ordination(
  audit,
  color = NULL,
  distance = NULL,
  aspect = c("auto", "equal")
)

Arguments

audit

A moat_audit object.

color

Optional single string naming a metadata variable. When NULL, the first batch variable is used when available, otherwise the outcome.

distance

Optional character vector naming audited distances to plot. When NULL, the first available distance is used. Use "all" to plot all audited distances.

aspect

A single string controlling panel aspect. "auto" uses the available plotting space and is easier to read when PC1 and PC2 have very different ranges. "equal" preserves a 1:1 coordinate ratio.

Value

A ggplot2::ggplot() object.

Examples

data("toy_moat")
audit <- moat(toy_moat, outcome = "outcome", batch = "batch", n_perm = 99)
plot_ordination(audit, color = "batch", distance = "bray")