teasdalm / rpca

R package for plotting SNP PCAs

rPCA

Some R functions to draw PCAs from smartpca and LASER data

Requires

• devtools
• tidyr
• ggplot2
• RColourBrewer

Install

• Commands to install.

devtools::install_github("teasdalm/rPCA")
library(rPCA)

Examples

• Read smartpca data and plot a PCA of reference data and samples.

tab <- read_evec("file.evec")
draw_pca_evec(tab, ids=c("Sample1", "Sample..n"))

• Read LASER data and plot a PCA of reference data and samples.

dat <- read.table("file.RefPC.coord", header = TRUE)
samples <- read.table("file.SeqPC.coord", header = TRUE)
draw_pca_laser(dat, samples)

• More help.

?draw_pca_evec
?draw_pca_laser