## ---- fig.show='hold'----------------------------------------------------
set.seed(1234)
library(svdvis)
B = c(runif(100, min=0, max=1), rep(0,400))
L = c(rep(1, 10), rep(-1, 10))
L = L / sd(L)
E = matrix(rnorm(500*20), nrow=500)
Y = B %*% t(L) + E
svd.obj = svd(Y)
colnames(svd.obj$v) = paste0("V",1:20)
rownames(svd.obj$v) = paste0("Sample",1:20)
## ------------------------------------------------------------------------
svd.scree(svd.obj, subr=5,
axis.title.x="Full scree plot", axis.title.y="% Var Explained")
## ------------------------------------------------------------------------
svd.scatter(svd.obj)
## ------------------------------------------------------------------------
svd.scatter(svd.obj, r=3, alpha=.5,
group=c(rep("Group 1", 10), rep("Group 2", 10)))
## ------------------------------------------------------------------------
svd.heatmap(svd.obj, r=5)
## ------------------------------------------------------------------------
svd.parallel(svd.obj, r=5, alpha=.5,
group=c(rep("Group 1", 10), rep("Group 2", 10)))
## ------------------------------------------------------------------------
svd.radial(svd.obj, r=3,
group=c(rep("Group 1", 10), rep("Group 2", 10)))
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