Test program for "pHom" package which can calculate persistent homologies in R

torus.R

library(phom)
library(scatterplot3d)

N <- 20
R <- 25
r <- 10
sd <- 1

ts <- seq(0,2*pi,pi/N)
ps <- seq(0,2*pi,pi/N)

x<-y<-z<-c()
for (t in ts) for (p in ps) {
  x <- c(x,R*cos(t)+r*cos(p)*cos(t))
  y <- c(y,R*sin(t)+r*cos(p)*sin(t))
  z <- c(z,r*sin(p))
}

par(mfcol=c(1,2))
scatterplot3d(x,y,z,type="l")

N1 <- length(ts)
rn <- function() rnorm(N1*N1,0,sd)
scatterplot3d(x+rn(),
              y+rn(),
              z+rn(),
              type="p",pch=20)

print("Please enter key for next graphs.")
readline()

par(mfcol=c(1,2))
max_dim <- 2
max_f <- 5
intervals <- pHom(cbind(x,y,z), max_dim, max_f)
plotBarcodeDiagram(intervals, 0, max_f, title="b0")
plotBarcodeDiagram(intervals, 1, max_f, title="b1")

print("Please enter key for next graphs.")
readline()

par(mfcol=c(1,1))
#plotBarcodeDiagram(intervals, 2, max_f)
plotPersistenceDiagram(intervals, max_dim, max_f)