plotAlluvial {SNFtool} | R Documentation |
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.
Author(s)
Daniel Cole
See Also
More information on Alluvial Package
Examples
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)
[Package SNFtool version 2.3.1 Index]