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MetaNet

MetaNet: Network analysis for multi-omics

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

Please go to https://asa12138.github.io/MetaNet_tutorial/ for the full vignette.

Installation

You can install the released version of MetaNet from CRAN with:

install.packages("MetaNet")

You can install the development version of MetaNet from GitHub with:

# install.packages("devtools")
devtools::install_github("Asa12138/MetaNet")

Citation

Please cite:

Chen Peng (2023). MetaNet: Network Analysis for Omics Data. R package, https://github.com/Asa12138/MetaNet.

Need helps?

If you have questions/issues, please visit MetaNet homepage first. Your problems are mostly documented.

If you think you found a bug, please post on github issue.

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Version

Install

install.packages('MetaNet')

Monthly Downloads

498

Version

0.1.2

License

GPL-3

Issues

0

Pull Requests

0

Stars

36

Forks

5

Maintainer

Peng Chen

Last Published

March 25th, 2024

Functions in MetaNet (0.1.2)

as_polycircle

Layout as a polycircle
cal_sim

Calculate similarity for one t(otutab)
check_tabs

Check tables and extract common samples
clean_igraph

Clean a igraph object
co_net

MetaNet networks
fit_power

Fit power-law distribution for an igraph
filter_n_module

Filter some modules as others
g_layout

Layout with group
df2net_tree

Transform a dataframe to a network edgelist.
rand_net_par

Net_pars of many random network
c_net_set

Set basic attributes from totu table
g_layout_polygon

Layout with group as a polygon
c_net_stability

Evaluate the stability of a network
c_net_plot

Plot a metanet
get_community

Get community
c_net_save

Save network file
get_module

Get module
fast_cor

Fast correlation calculation
input_corr

Import corr from .csv file
get_module_eigen

Get module_eigen
get_group_skeleton

Get skeleton network according to a group
extract_sub_net

Extract sub-network from the whole network
input_gephi

Input a graphml file exported by Gephi
metab

MetaNet networks abundance
get_e

Get edge information
micro_g

MetaNet networks metadata
micro

MetaNet networks abundance
olympic_rings_net

Plot olympic rings using network
module_eigen

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

Plot a metanet
module_detect

Detect the modules
plot.rmt_res

Plot a rmt_res
get_n

Get network information
multi_net_build

Multi-omics network build
nc

Calculate natural_connectivity
print.cohesion

Print method for 'cohesion' objects
metab_g

MetaNet networks metadata
print.robustness

Print method for 'robustness' objects
print.ggig

Print method for 'ggig' objects
p.adjust.table

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

Quick build a metanet from two columns table
venn_net

Venn network
print.vulnerability

Print method for 'vulnerability' objects
print.corr

Print method for 'corr' objects
show_MetaNet_logo

Show MetaNet logo
plot.robustness

Plot robustness
smallworldness

Calculate small-world coefficient
multi1

MetaNet networks
net_par

Calculate all topological indexes of a network
module_net

Generate a n-modules network
c_net_filter

Filter a network according to some attributes
c_net_union

Union two networks
netD3plot

plot use networkD3
summ_2col

Summaries two columns information
print.coors

Print method for 'coors' objects
transc

MetaNet networks abundance
%>%

Pipe operator
c_net_update

Update a metanet object or transform igraph object to metanet object
co_net2

MetaNet networks
transc_g

MetaNet networks metadata
co_net_rmt

MetaNet networks
%<>%

Assignment pipe
get_v

Get vertex information
is_metanet

Is this object a metanet object?
plot.robust

Plot robust
plot.ggig

Plot a ggig
rand_net

Degree distribution comparison with random network
summary_module

Summary module index
to_module_net

Transformation a network to a module network
print.robust

Print method for 'robust' objects
print.metanet

Print method for 'metanet' objects
links_stat

Link summary of the network
plot.vulnerability

Plot vulnerability
zp_analyse

Zi-Pi calculate
as_arc

Layout as a arc
anno_edge

Use dataframe to annotate edges of an igraph
arc_count

Edgelist
Cohesion

Cohesion calculation
MetaNet-package

MetaNet: Network Analysis for Omics Data
RMT_threshold

Get RMT threshold for a correlation matrix
as_circle_tree

Layout as a circle_tree
anno_vertex

Use data.frame to annotate vertexes of metanet
arc_taxonomy

Edgelist
as.ggig

Transfer an igraph object to a ggig
as_line

Layout as a line
as_polygon

Layout as a polygon
as_polyarc

Layout as a polyarc
c_net_layout

Layout coordinates
c_net_build

Construct a metanet from a corr object
c_net_annotate

Annotate a metanet
c_net_calculate

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

Construct a network from edge_list dataframe