SNFtool (version 2.3.1)

plotAlluvial: Plot Alluvial

Description

This function plots an alluvial (Parallel coordinate plot) of sample clusterings for a specified number of clusters. Samples can be coloured by providing a vector of colours, allowing for the visualization of sample properties over a range of clustering number choices.

*This is a wrapper function calling the Alluvial Package (Bojanowski M. & Edwards R)

Usage

plotAlluvial(W, clust.range, color.vect)

Arguments

W

Affinity matrix of dimension n.samples by n.samples

clust.range

Integer vector specifying the number of clusters for each clustering

color.vect

A vector of color's of length n.samples to colour the samples

Value

Plots an alluvial plot for range of clustering choices.

See Also

More information on Alluvial Package

Examples

# NOT RUN {
K <- 20
alpha <- 0.5
iter <- 20

data(Data1)
data(Data2)

dist1 <- (dist2(as.matrix(Data1), as.matrix(Data1)))^(1/2)
dist2 <- (dist2(as.matrix(Data2), as.matrix(Data2)))^(1/2)

W1 <- affinityMatrix(dist1, K, alpha)
W2 <- affinityMatrix(dist2, K, alpha)

W <- SNF(list(W1, W2), K, iter)

#Plots the alluvial with no colouring
plotAlluvial(W, 2:5)

#Change the colour of all samples a single colour
plotAlluvial(W, 2:5, col="red")

colour.breaks <- 30
#This will assign each sample to one of colour.breaks colour bins between green and red.
colFunc <- colorRampPalette(c("green", "red"))
colours <- colFunc(colour.breaks)[as.numeric(cut(Data1[,1],breaks=colour.breaks))]
plotAlluvial(W, 2:5, col=colours)
# }