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MetaNet

MetaNet: Network analysis for multi-omics

The HTML documentation of the latest version is available at Github page.

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Install

install.packages('MetaNet')

Monthly Downloads

247

Version

0.2.7

License

GPL-3

Issues

1

Pull Requests

0

Stars

59

Forks

7

Maintainer

Peng Chen

Last Published

June 26th, 2025

Functions in MetaNet (0.2.7)

cal_sim

Calculate similarity for one t(otutab)
c_net_highlight

Highlight specific nodes in a network
c_net_build

Construct a metanet from a corr object
as_polyarc

Layout as a polyarc
c_net_layout

Layout coordinates
c_net_stability

Evaluate the stability of a network
c_net_load

Load network file
filter_n_module

Filter some modules as others
c_net_set

Set basic attributes from totu table
get_v

Get vertex information
fast_cor

Fast correlation calculation
get_n

Get network information
rand_net_par

Net_pars of many random network
g_layout_polygon

Layout with group as a polygon
micro

MetaNet networks abundance
check_tabs

Check tables and extract common samples
get_community

Get community
co_net_rmt

MetaNet networks
metab_g

MetaNet networks metadata
links_stat

Link summary of the network
metab

MetaNet networks abundance
net_par

Calculate all topological indexes of a network
module_eigen

Calculate the eigenvalue of each module and correlation of nodes and eigenvalue (node_eigen_cor).
plot_multi_nets

Batch drawing multiple network diagrams
get_group_skeleton

Get skeleton network according to a group
c_net_compare

Compare Two Networks
c_net_calculate

Calculate correlation for one or two t(otutab), or distance for one t(otutab).
print.metanet_compare

Print method for 'metanet_compare' objects
print.robust

Print method for 'robust' objects
get_e

Get edge information
plot_e_type_bar

Plot e_type bar
module_net

Generate a n-modules network
c_net_intersect

Intersect two networks
df2net_tree

Transform a dataframe to a network edgelist.
c_net_difference

Difference two networks
extract_sample_net

Extract each sample network from the whole network
c_net_ego

Extract ego-centric subnetwork with preserved class attributes
c_net_save

Save network file
c_net_plot

Plot a metanet
clean_igraph

Clean a igraph object
clean_multi_edge_metanet

Clean multi edge metanet to plot
olympic_rings_net

Plot olympic rings using network
plot.ggig

Plot a ggig
module_detect

Detect the modules
co_net

MetaNet networks
input_gephi

Input a graphml file exported by Gephi
co_net2

MetaNet networks
g_layout_nice

Layout with group nicely
g_layout_poly_sector

Layout with group
is_metanet

Is this object a metanet object?
micro_g

MetaNet networks metadata
plot.metanet

Plot a metanet
plot.robustness

Plot robustness
plot.robust

Plot robust
plot.metanet_compare

Plot a metanet_compare
p.adjust.table

p.adjust apply on a correlation table (matrix or data.frame)
%>%

Pipe operator
rand_net

Degree distribution comparison with random network
summary_module

Summary module index
read_corr

Read a corr object
to_module_net

Transformation a network to a module network
print.corr

Print method for 'corr' objects
print.coors

Print method for 'coors' objects
nc

Calculate natural_connectivity
venn_net

Venn network
save_corr

Save a corr object
show_MetaNet_logo

Show MetaNet logo
plot.vulnerability

Plot vulnerability
plot.rmt_res

Plot a rmt_res
zp_analyse

Zi-Pi calculate
transc

MetaNet networks abundance
print.robustness

Print method for 'robustness' objects
print.vulnerability

Print method for 'vulnerability' objects
transc_g

MetaNet networks metadata
netD3plot

plot use networkD3
plot_net_degree

Plot degree distribution of networks
smallworldness

Calculate small-world coefficient
transform_coors

Transform the layout of a 'coors' object
print.cohesion

Print method for 'cohesion' objects
spatstat_layout

Generate spatial layout using spatstat
twocol_edgelist

Quick build a metanet from two columns table
as_polycircle

Layout as a polycircle
as_polygon

Layout as a polygon
input_cytoscape

Input a cyjs file exported by Cytoscape
fit_power

Fit power-law distribution for an igraph
c_net_union

Union two networks
g_layout

Layout with group
%<>%

Assignment pipe
get_module_eigen

Get module_eigen
get_module

Get module
c_net_update

Update a metanet object or transform igraph object to metanet object
multi_net_build

Multi-omics network build
print.ggig

Print method for 'ggig' objects
multi1

MetaNet networks
print.metanet

Print method for 'metanet' objects
summ_2col

Summaries two columns information
summary.corr

Summary method for 'corr' objects
arc_taxonomy

Edgelist
Cohesion

Cohesion calculation
anno_edge

Use dataframe to annotate edges of an igraph
as.ggig

Transfer an igraph object to a ggig
adjacency_similarity

Calculate Similarity Between Two Graphs via Adjacency Matrices
anno_vertex

Use data.frame to annotate vertexes of metanet
RMT_threshold

Get RMT threshold for a correlation matrix
as_arc

Layout as a arc
arc_count

Edgelist
MetaNet-package

MetaNet: Network Analysis for Omics Data
as_coors

Transfer to a coors object
as_line

Layout as a line
as_circle_tree

Layout as a circle_tree
as_multi_layer

Layout as a multi_layer
as_poly_sector

Layout as a multi_layer
c_net_annotate

Annotate a metanet
c_net_filter

Filter a network according to some attributes
c_net_from_edgelist

Construct a network from edge_list dataframe