filter_n_module: Filter some modules as others

In MetaNet: Network Analysis for Omics Data

Filter some modules as others

Description

Filter some modules as others

Combine or cut modules to module_number

Plot module tree

Usage

filter_n_module(go_m, n_node_in_module = 0, keep_id = NULL, delete = FALSE)

combine_n_module(go_m, module_number = 5)

plot_module_tree(go_m, module = "module", community = NULL, label.size = 2)

Arguments

go_m	module metanet
n_node_in_module	transfer the modules less than n_node_in_module to "others"
keep_id	keep modules ids, will not be "others"
delete	logical, delete others modules? default:FALSE, the others module will be "others".
module_number	number of modules
module	which column name is module. default: "module"
community	community object, default: NULL, use the community of go_m
label.size	label.size

Value

metanet with modules

ggplot

See Also

Other module: get_community(), get_module_eigen(), get_module(), module_detect(), module_eigen(), module_net(), summary_module(), to_module_net(), zp_analyse()

Examples

data("c_net")
module_detect(co_net) -> co_net_modu
filter_n_module(co_net_modu, n_node_in_module = 30) -> co_net_modu
if (requireNamespace("ggtree") && requireNamespace("treeio")) plot_module_tree(co_net_modu)
combine_n_module(co_net_modu, 20) -> co_net_modu1
if (requireNamespace("ggtree") && requireNamespace("treeio")) plot_module_tree(co_net_modu1)

MetaNet documentation built on May 29, 2024, 1:21 a.m.