plot_pca: plot_pca
In limnoliver/pah: Common Analyses for Polycyclic Aromatic Hydrocarbons (PAH) Data

Creates various plots from the PCA components as well as the calculated PCA Euclidean distances.

1 2	plot_pca(pca_dat, plot_type = "distance_boxplot", source_abbreviation = FALSE, pah_sources = sources)

`pca_dat`	The output from 'pah_pca' which includes the component data as well as the calculated Euclidean distances data.
`plot_type`	Which plot to create. Options include 'distance_boxplot' which summarizes the Euclidean distances by source, 'pca_components' which shows where the sources and samples lie in all combinations of the chosen components space.
`source_abbreviation`	logical, whether source abbreviations should be used when plot_type = 'distance_boxplot'.
`pah_sources`	a dataframe of source profiles. The default is to use the built-in 'source_profiles' table, but users can provide their own table. This is useful if the user has a source profile to add to the built-in table.

If plot_type = 'distance_boxplot', a single boxplot is returned with source IDs on the x axis and Euclidean distances on the y axis. If plot_type = 'pca_components', a scatterplot of all possible combinations of chosen components are included in a panel matrix, with samples as black dots and sources as red dots that are labeled with the source abbreviation. To see the full names of each source abbrevation, see table source_ratios.

limnoliver/pah documentation built on April 30, 2020, 2:45 p.m.