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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

498

Version

0.2.5

License

GPL-3

Issues

0

Pull Requests

0

Stars

37

Forks

5

Maintainer

Peng Chen

Last Published

April 10th, 2025

Functions in MetaNet (0.2.5)

c_net_filter

Filter a network according to some attributes
as_polygon

Layout as a polygon
c_net_calculate

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

Load network file
c_net_layout

Layout coordinates
c_net_from_edgelist

Construct a network from edge_list dataframe
c_net_annotate

Annotate a metanet
c_net_set

Set basic attributes from totu table
extract_sample_net

Extract each sample network from the whole network
as_polyarc

Layout as a polyarc
c_net_stability

Evaluate the stability of a network
df2net_tree

Transform a dataframe to a network edgelist.
c_net_save

Save network file
clean_multi_edge_metanet

Clean multi edge metanet to plot
as_poly_sector

Layout as a multi_layer
as_multi_layer

Layout as a multi_layer
g_layout

Layout with group
fit_power

Fit power-law distribution for an igraph
clean_igraph

Clean a igraph object
c_net_plot

Plot a metanet
links_stat

Link summary of the network
as_coors

Transfer to a coors object
g_layout_polygon

Layout with group as a polygon
get_community

Get community
print.coors

Print method for 'coors' objects
co_net_rmt

MetaNet networks
module_eigen

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

Print method for 'corr' objects
module_net

Generate a n-modules network
as_line

Layout as a line
g_layout_nice

Layout with group nicely
g_layout_poly_sector

Layout with group
print.vulnerability

Print method for 'vulnerability' objects
metab

MetaNet networks abundance
rand_net

Degree distribution comparison with random network
check_tabs

Check tables and extract common samples
c_net_union

Union two networks
get_module

Get module
cal_sim

Calculate similarity for one t(otutab)
get_module_eigen

Get module_eigen
c_net_update

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

Layout as a polycircle
co_net

MetaNet networks
rand_net_par

Net_pars of many random network
micro_g

MetaNet networks metadata
net_par

Calculate all topological indexes of a network
%<>%

Assignment pipe
input_cytoscape

Input a cyjs file exported by Cytoscape
spatstat_layout

Generate spatial layout using spatstat
olympic_rings_net

Plot olympic rings using network
transc_g

MetaNet networks metadata
transform_coors

Transform the layout of a 'coors' object
co_net2

MetaNet networks
read_corr

Read a corr object
smallworldness

Calculate small-world coefficient
plot.robust

Plot robust
module_detect

Detect the modules
show_MetaNet_logo

Show MetaNet logo
summ_2col

Summaries two columns information
get_e

Get edge information
plot.vulnerability

Plot vulnerability
multi1

MetaNet networks
get_group_skeleton

Get skeleton network according to a group
get_v

Get vertex information
get_n

Get network information
zp_analyse

Zi-Pi calculate
nc

Calculate natural_connectivity
netD3plot

plot use networkD3
metab_g

MetaNet networks metadata
fast_cor

Fast correlation calculation
is_metanet

Is this object a metanet object?
micro

MetaNet networks abundance
input_gephi

Input a graphml file exported by Gephi
plot.rmt_res

Plot a rmt_res
filter_n_module

Filter some modules as others
p.adjust.table

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

Pipe operator
multi_net_build

Multi-omics network build
plot.ggig

Plot a ggig
plot.metanet

Plot a metanet
print.robustness

Print method for 'robustness' objects
print.robust

Print method for 'robust' objects
summary.corr

Summary method for 'corr' objects
print.cohesion

Print method for 'cohesion' objects
print.ggig

Print method for 'ggig' objects
plot.robustness

Plot robustness
save_corr

Save a corr object
to_module_net

Transformation a network to a module network
print.metanet

Print method for 'metanet' objects
transc

MetaNet networks abundance
summary_module

Summary module index
venn_net

Venn network
twocol_edgelist

Quick build a metanet from two columns table
anno_vertex

Use data.frame to annotate vertexes of metanet
as_arc

Layout as a arc
Cohesion

Cohesion calculation
arc_taxonomy

Edgelist
as_circle_tree

Layout as a circle_tree
anno_edge

Use dataframe to annotate edges of an igraph
RMT_threshold

Get RMT threshold for a correlation matrix
arc_count

Edgelist
as.ggig

Transfer an igraph object to a ggig
c_net_build

Construct a metanet from a corr object
MetaNet-package

MetaNet: Network Analysis for Omics Data