plotInteractions: Plot pdCor TF-TF interactions

In tallulandrews/scTarNet: Single-cell Targetted Network Inference

Description

Plot the TF-TF interactions calculated by calculateConditionalCors

Usage

plotInteractions(combined_interactions, recurr_threshold=max(combined_interactions$pair2consistent[,3])/2, target_threshold=1, suppress.plot=FALSE, seed.col="dodgerblue", interaction.col="black", rnd.seed=2948)

Arguments

combined_interactions	Output from combineInteractions
recurr_threshold	number of each particular a correlation must be seen.
target_threshold	minimum number of targets to keep an interaction.
suppress.plot	whether to plot the network
seed.col	colour of seed TF nodes
interaction.col	colour of edges for TF-TF interactions
rnd.seed	random number generator seed, to ensure reproducible plots.

Details

Filters TF-TF interactions 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)
	pair2targets <- data.frame(TF1=sample(c("A", "B", "C"), 20, replace=TRUE), TF2=sample(c("A", "B", "C"), 20, replace=TRUE), Targets=sample(c("D", "E", "F", "G", "H"), 20, replace=TRUE))
	pair2targets <- unique(pair2targets);
	pair2targets$recurr <- rpois(nrow(pair2targets), lambda=1)+1

	pair2consistent <- pair2targets[,1:2]
	pair2consistent <- unique(pair2consistent);
	pair2consistent$recurr <- rpois(nrow(pair2consistent), lambda=1)+1

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

	plotInteractions(interactions_out, recurr_threshold=2, suppress.plot=TRUE)

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