pca.plot | R Documentation |

Ordination of Principal Components from the output of a Principal Components Analysis performed by `prcomp`

function (`stats`

package). Require a `factor`

object with `groups`

, which enable the plot to feature colored groups and convex hulls (if desired).

```
pca.plot(
PCA.out = NULL,
groups = NULL,
col.gp = grDevices::rainbow(length(levels(groups))),
conv.hulls = NULL,
col.conv = grDevices::rainbow(length(levels(conv.hulls))),
PCs = c(1, 2),
main = "Ordination of PCA coordinates",
sp.as = "points",
sp.text = NULL,
cross.origin = TRUE,
lwd = 1,
lty = "dotted",
leg = TRUE,
leg.labels = groups,
leg.pos = "topright",
cex.leg = 1,
cex = 1,
cex.axis = 1,
cex.lab = 1,
cex.main = 1
)
```

`PCA.out` |
the output of a Principal Components Analysis performed by |

`groups` |
groups to use as colors and/or convex hulls. Must be a |

`col.gp` |
a |

`conv.hulls` |
groups to use for convex hulls. Must be a |

`col.conv` |
a |

`PCs` |
a vector of length two with the Principal Components intended for the plot. By default: |

`main` |
main title of output plot. Should be presented between quotation marks. By default: |

`sp.as` |
enables one to choose between ploting elements as |

`sp.text` |
only applies when |

`cross.origin` |
A logical. If |

`lwd` |
only applies when |

`lty` |
only applies when |

`leg` |
a logical. If |

`leg.labels` |
only applies when |

`leg.pos` |
only applies when |

`cex.leg` |
only applies when |

`cex` |
same as in |

`cex.axis` |
same as in |

`cex.lab` |
same as in |

`cex.main` |
same as in |

Require the output of `prcomp`

and a vector with `groups`

to plot. In addition, it is also possible to include convex hulls around each group (i.e. `conv.hulls`

) and to control the colors intended for each group (i.e. `col.gp`

) and for each convex hull (i.e. `col.conv`

).

Pedro Rocha

Rocha, P. & Romano, P. (2021) The shape of sound: A new `R`

package that crosses the bridge between Bioacoustics and Geometric Morphometrics. *Methods in Ecology and Evolution, 12*(6), 1115-1121.

`prcomp`

, `palette`

, `rgb`

, `rainbow`

, `legend`

Useful links:

```
data(eig.sample)
# PCA using 3D semilandmark coordinates
pca.eig.sample <- stats::prcomp(geomorph::two.d.array(eig.sample))
# Verify names for each acoustic unit and the order in which they appear
dimnames(eig.sample)[[3]]
# Create factor to use as groups in subsequent ordination plot
sample.gr <- factor(c(rep("centralis", 3), rep("cuvieri", 3), rep("kroyeri", 3)))
# Clear current R plot to prevent errors
grDevices::dev.off()
# Plot result of Principal Components Analysis
pca.plot(PCA.out = pca.eig.sample, groups = sample.gr, conv.hulls = sample.gr,
main="PCA of 3D coordinates", leg=TRUE, leg.pos = "top")
```

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