get_nets {fcoex} | R Documentation

## Network visualization

### 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)

[Package fcoex version 1.8.0 Index]