In [1]:

    

require(fastcluster) 
library(TDAmapper)
library(devtools)
library(igraph)


    

    




Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

    hclust


Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

In [15]:

    

# sample points from two intertwined spirals
set.seed("1")
t <- runif(100, min=1, max=6.3) # theta
X <- data.frame( x = c( t*cos(t), -t*cos(t) ), y = c( t*sin(t), -t*sin(t) ) )
d <- dist(X)
plot(X[,1], X[,2])
X


    

    






x
y

	
-1.7867054
 1.6131571
	
-2.9297442
 0.5009081
	
-2.5261500
-3.1478332
	
 5.1839651
-2.6312171
	
-0.9884714
 1.8175067
	
 4.9949788
-2.8713532
	
 5.7787757
-1.6392512
	
-0.9392416
-4.4031676
	
-1.5999694
-4.0281873
	
 0.3198333
 1.2883617
	
-1.0408838
 1.8142835
	
-0.6908825
 1.8082623
	
-0.3300272
-4.6294725
	
-3.0187612
 0.3207131
	
 1.8265000
-4.7404555
	
-3.1990564
-1.7319558
	
 0.4364523
-4.7835082
	
 6.2549740
-0.1631855
	
-2.9897559
 0.3829880
	
 2.0319990
-4.7000093
	
 5.6341273
-1.9250933
	
-1.1168120
 1.8071017
	
-1.1386236
-4.3058684
	
-0.1573917
 1.6579882
	
-1.8080585
 1.6028983
	
-3.0326138
 0.2895433
	
 0.5132877
 0.9399520
	
-3.0066865
 0.3471078
	
 4.3833873
-3.5001217
	
-2.6454461
 0.9290792
	
⋮
⋮
	
 2.6327364 
-0.94466515
	
-3.6606962 
 4.03624496
	
 2.7071729 
-0.84981239
	
 2.5790235 
-1.00798719
	
 3.2692009 
 1.31740832
	
-4.8701889 
 3.01640580
	
-4.2607135 
 3.60470140
	
 3.0584035 
-0.22872894
	
-2.0286352 
 4.70074337
	
-5.9794502 
 1.16181393
	
 3.2603842 
 0.53319531
	
-0.3051847 
 4.76656790
	
 3.1192408 
-0.06745629
	
 2.4906606 
-1.10398466
	
-1.4821413 
 4.78842708
	
 1.0007729 
-1.81687791
	
-0.2695566 
 4.76131826
	
 0.1218968 
-1.64044451
	
 1.5350285 
-1.71426333
	
 0.3300824 
-1.72827438
	
 1.4610766 
-1.73733077
	
-0.3354066 
-1.26876740
	
 1.3362224 
 4.19652847
	
-4.5307186 
 3.36598952
	
-2.0716875 
 4.69116579
	
-2.5663399 
 4.55216701
	
 3.2880634 
 0.91482131
	
 3.1718359 
 0.10106661
	
-2.9263244 
 4.41603003
	
 2.0395373 
 3.67858063









    

In [9]:

    

filter <- X[,2] # height projection
num_intervals <- 10
percent_overlap <- 50
num_bins_when_clustering <- 10

m3 <- mapper1D(
	distance_matrix = d, 
	filter_values = filter,	
	# num_intervals = 10, # use default
	# percent_overlap = 50, # use default
	# num_bins_when_clustering = 10 # use default
	)
    
g3 <- graph.adjacency(m3$adjacency, mode="undirected")
plot(g3, layout = layout.auto(g3) )


    

In [10]:

    

# parametrize a trefoil knot
n <- 100
t <- 2*pi*(1:n)/n
X <- data.frame(x = sin(t)+2*sin(2*t),
                y = cos(t)-2*cos(2*t),
                z = -sin(3*t))
f <- X

library(rgl)
plot3d(X$x, X$y, X$z)


    

    




Error in library(rgl): there is no package called ‘rgl’
Traceback:

1. library(rgl)
2. stop(txt, domain = NA)

In [13]:

    

# use the github version so that vertices stay on the canvas
library(devtools)
devtools::install_github("christophergandrud/networkD3")
library(networkD3)


    

    




Downloading GitHub repo christophergandrud/networkD3@master
from URL https://api.github.com/repos/christophergandrud/networkD3/zipball/master
Installing networkD3
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL  \
  '/tmp/RtmpYukpUP/devtools514f28325bd1/christophergandrud-networkD3-1d217fb'  \
  --library='/home/raula-k/R/x86_64-pc-linux-gnu-library/3.2' --install-tests 

In [14]:

    

# parametrize a trefoil knot
n <- 100
t <- 2*pi*(1:n)/n
X <- data.frame(x = sin(t)+2*sin(2*t),
                y = cos(t)-2*cos(2*t),
                z = -sin(3*t))
f <- X

m5 <- mapper(dist(X), f, c(3,3,3), c(30,30,30), 5)
g5 <- graph.adjacency(m5$adjacency, mode="undirected")
plot(g5, layout = layout.auto(g5) )
tkplot(g5)

# create data frames for vertices and edges with the right variable names 
MapperNodes <- mapperVertices(m5, 1:dim(f)[1] )
MapperLinks <- mapperEdges(m5)

# interactive plot
forceNetwork(Nodes = MapperNodes, Links = MapperLinks, 
            Source = "Linksource", Target = "Linktarget",
            Value = "Linkvalue", NodeID = "Nodename",
            Group = "Nodegroup", opacity = 0.8, 
            linkDistance = 10, charge = -400)


    

    





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