scatter_plot: Create a scatterplot showing correlation between specific...

In FrankD/nethet: A bioconductor package for high-dimensional exploration of biological network heterogeneity

Description

This function takes the output of het_cv_glasso or mixglasso and creates a plot showing the correlation between specified node pairs in the network for all groups. The subplots for each node pair are arranged in a numPairs by numGroups grid. Partial correlations associated with each node pair are also displayed.

Usage

scatter_plot(net.clustering, data, node.pairs, display = TRUE,
  node.names = rownames(net.clustering$Mu),
  group.names = sort(unique(net.clustering$comp)), cex = 1)

Arguments

net.clustering	A network clustering object as returned by het_cv_glasso or mixglasso.
data	Observed data for the nodes, a numObs by numNodes matrix. Note that nodes need to be in the same ordering as in node.names.
node.pairs	A matrix of size numPairs by 2, where each row contains a pair of nodes to display. If node.names is specified, names in node.pairs must correspond to elements of node.names.
display	If TRUE, print the plot to the current output device.
node.names	Names for the nodes in the network. If NULL, names from net.clustering will be used.
group.names	Names for the clusters or groups. If NULL, names from net.clustering will be used (by default these are integets 1:numClusters).
cex	Scale factor for text and symbols in plot.

Value

Returns a ggplot2 object. If display=TRUE, additionally displays the plot.

Examples

n = 500
p = 10
s = 0.9
n.comp = 3

# Create different mean vectors
Mu = matrix(0,p,n.comp)

# Define non-zero means in each group (non-overlapping)
nonzero.mean = split(sample(1:p),rep(1:n.comp,length=p))

# Set non-zero means to fixed value
for(k in 1:n.comp){
	Mu[nonzero.mean[[k]],k] = -2/sqrt(ceiling(p/n.comp))
}

# Generate data
sim.result = sim_mix_networks(n, p, n.comp, s, Mu=Mu)
mixglasso.result = mixglasso(sim.result$data, n.comp=3)
mixglasso.clustering = mixglasso.result$models[[mixglasso.result$bic.opt]]

# Specify edges
node.pairs = rbind(c(1,3), c(6,9),c(7,8))

# Create scatter plots of specified edges
scatter_plot(mixglasso.clustering, data=sim.result$data,
					 node.pairs=node.pairs)

FrankD/nethet documentation built on Oct. 5, 2020, 8:22 a.m.