get_nets: Network visualization

In csbl-usp/fcoex: FCBF-based Co-Expression Networks for Single Cells

Description

Creates network visualizations based on the adjacency matrix obtained with the find_cbf_modules method

Usage

get_nets(fc, n = 10, min_elements = 5, ...)

## S4 method for signature 'fcoex'
get_nets(fc, n = 10, min_elements = 5, ...)

Arguments

fc	Object of class fcoex.
n	number of nodes to label
min_elements	Minimum number of elements in a module for it to be plotted. Defaults to 5.
...	Optional parameters.

Details

This function was copied and adapted from the CEMiTool package. The visualization of networks in this function is derivative of the intelectual work of CEMiTool's authors.

Value

Object of class fcoex with profile plots

Examples

library(SingleCellExperiment)
data("mini_pbmc3k")
targets <- colData(mini_pbmc3k)$clusters
exprs <- as.data.frame(assay(mini_pbmc3k, "logcounts"))
fc <- new_fcoex(exprs, targets)
fc <- discretize(fc)
fc <- find_cbf_modules(fc)
fc <- get_nets(fc)

csbl-usp/fcoex documentation built on Sept. 15, 2021, 7:42 a.m.