plotInteractionsWithTargets: Plot pdCor TF-TF interactions with their targets

In tallulandrews/scTarNet: Single-cell Targetted Network Inference

Description

Plot the gene-gene correlations inferred by calculateTFstoTargets, which are targets of the TF-TF interactions inferred by calculateConditionalCors.

Usage

plotInteractionsWithTargets(combined_dependencies, combined_interactions, recurr_threshold=max(combined_interactions$pair2consistent[,3])/2, suppress.plot=FALSE, seed.col="dodgerblue", target.col="goldenrod1", interaction.col="black", edge.col=c("blue", "grey45", "red"), rnd.seed=2948)

Arguments

combined_dependencies	Output from combineDependencies
combined_interactions	Output from combineInteractions
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
interaction.col	colour of edges for TF-TF interactions
edge.col	colour of edges for negative, other, and positive correlations
rnd.seed	random number generator seed, to ensure reproducible plots.

Details

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

Value

list of a dataframe 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=rep(c("A", "B", "C"), times=3), Targets=rep(c("D", "E", "F"), each=3))
        dependencies_out$recurr <- rpois(nrow(dependencies_out), lambda=1)+1
        dependencies_out$direction <- sample(c(-1, 0, 1), nrow(dependencies_out), replace=TRUE)

	pair2targets <- data.frame(TF1=c("A", "A", "B", "B"), TF2=sample(c("B", "C", "C", "C"), 20, replace=TRUE), Targets=c("D", "E", "E", "F")) # Nope this will still create novel TF-Target pairs
	pair2targets$recurr <- rpois(nrow(pair2targets), lambda=1)+1

	pair2consistent <- data.frame(TF1=c("A","A","B"), TF2=c("B", "C", "C"))
	pair2consistent$recurr <- rpois(nrow(pair2consistent), lambda=1)+1

	interactions_out <- list(pair2targets=pair2targets, pair2consistent=pair2consistent);

	plotInteractionsWithTargets(dependencies_out, interactions_out, recurr_threshold=2, suppress.plot=TRUE)

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