plotDependencies: Plot dCor gene-gene correlations

In tallulandrews/scTarNet: Single-cell Targetted Network Inference

Description

Plot the gene-gene correlations inferred by calculateTFstoTargets.

Usage

	plotDependencies(combined_dependencies, recurr_threshold=max(combined_dependencies$recurr)/2, suppress.plot=FALSE, seed.col="dodgerblue", target.col="goldenrod1", edge.col=c("blue", "black", "red"), rnd.seed=2948)

Arguments

combined_dependencies	Output from combineDependencies
recurr_threshold	number of each particular a correlation must be seen.
suppress.plot	whether to plot the network
seed.col	colour of seed TF nodes
target.col	colour of target nodes
edge.col	colour of edges for negative, other, and positive correlations
rnd.seed	random number generator seed, to ensure reproducible plots.

Details

Filters TF-Target relationships based on the frequency it was observed across replicates. Plots the resulting network using igraph with colour coded nodes and edges.

Value

list of the edgelist of the network as a data.frame and the igraph object of the network.

See Also

igraph.plotting

Examples

	set.seed(101)
	dependencies_out <- data.frame(Gene=sample(c("A", "B", "C"), 20, replace=TRUE), Targets=sample(c("D", "E", "F", "G", "H"), 20, replace=TRUE))
	dependencies_out <- unique(dependencies_out);
	dependencies_out$recurr <- rpois(nrow(dependencies_out), lambda=1)+1
	dependencies_out$direction <- sample(c(-1, 0, 1), nrow(dependencies_out), replace=TRUE)

	plotDependencies(dependencies_out, recurr_threshold=2, suppress.plot=TRUE)

tallulandrews/scTarNet documentation built on May 31, 2019, 2:27 p.m.