pep.pca.plot: Plot LAPP PCA
In ParhamLab/PeptidePCA: PCA using physicochemical properties of HLA

Description Usage Arguments

pep.pca.plot() takes in a modified PCA object returned by pep.pca() and plots it. Uses ggplot2.

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pep.pca.plot(pca, dim1 = 1, dim2 = 2, type = "density",
  colors = c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2",
  "#D55E00", "#CC79A7"))

`pca`	modified PCA object returned by pep.pca(). Can take up to 8 different HLA alleles.
`dim1`	Index of PC to plot along the x-axis. Defaults to 1
`dim2`	Index of PC to plot along the y-axis. Defaults to 2
`type`	Describes the type of plot to make. Either 'points' (default) for scatter plo,t or 'density' for a 2D KDE density graph.
`colors`	character that describes how each of the clusters should be colored. Defaults to the colorblind palette proposed by Okabe and Ito (2002) http://jfly.iam.u-tokyo.ac.jp/color/
`type`	How the PCA should be plotted. Either 'points' for scatterplot or 'density' for an automated 2D KDE plot (default).