get_nets {fcoex} | R Documentation |
Creates network visualizations based on the adjacency matrix obtained with the find_cbf_modules method
get_nets(fc, n = 10, min_elements = 5, ...) ## S4 method for signature 'fcoex' get_nets(fc, n = 10, min_elements = 5, ...)
fc |
Object of class |
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. |
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.
Object of class fcoex
with profile plots
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)