# Network Analysis for Omics Data

## Documentation for package ‘MetaNet’ version 0.3.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D E F G I L M N O P R S T V Z

## -- A --

adjacency_similarity | Calculate Similarity Between Two Graphs via Adjacency Matrices
anno_edge | Use dataframe to annotate edges of an igraph
anno_node | Use data.frame to annotate vertexes of metanet
anno_vertex | Use data.frame to annotate vertexes of metanet
arc_count | Edgelist
arc_taxonomy | Edgelist
as.ggig | Transfer an igraph object to a ggig
as.metanet | Update a metanet object or transform igraph object to metanet object
as_arc | Layout as a arc
as_circle_tree | Layout as a circle_tree
as_coors | Transfer to a coors object
as_line | Layout as a line
as_multi_layer | Layout as a multi_layer
as_polyarc | Layout as a polyarc
as_polycircle | Layout as a polycircle
as_polygon | Layout as a polygon
as_poly_sector | Layout as a multi_layer

## -- C --

cal_sim | Calculate similarity for one t(otutab)
check_tabs | Check tables and extract common samples
clean_igraph | Clean a igraph object
clean_multi_edge_metanet | Clean multi edge metanet to plot
Cohesion | Cohesion calculation
combine_n_module | Filter some modules as others
compare_rand | Net_pars of many random network
co_net | MetaNet networks
co_net2 | MetaNet networks
co_net_rmt | MetaNet networks
c_net_annotate | Annotate a metanet
c_net_build | Construct a metanet from a corr object
c_net_cal | Calculate correlation for one or two t(otutab), or distance for one t(otutab).
c_net_calculate | Calculate correlation for one or two t(otutab), or distance for one t(otutab).
c_net_compare | Compare Two Networks
c_net_difference | Difference two networks
c_net_ego | Extract ego-centric subnetwork with preserved class attributes
c_net_filter | Filter a network according to some attributes
c_net_from_edgelist | Construct a network from edge_list dataframe
c_net_highlight | Highlight specific nodes in a network
c_net_index | Calculate all topological indexes of a network
c_net_intersect | Intersect two networks
c_net_lay | Layout coordinates
c_net_layout | Layout coordinates
c_net_load | Load network file
c_net_module | Detect the modules
c_net_neighbors | Extract ego-centric subnetwork with preserved class attributes
c_net_plot | Plot a metanet
c_net_save | Save network file
c_net_set | Set basic attributes from totu table
c_net_skeleton | Get skeleton network according to a group
c_net_stability | Evaluate the stability of a network
c_net_union | Union two networks
c_net_update | Update a metanet object or transform igraph object to metanet object

## -- D --

df2net_tree | Transform a dataframe to a network edgelist.

## -- E --

extract_sample_net | Extract each sample network from the whole network

## -- F --

fast_cor | Fast correlation calculation
filter_n_module | Filter some modules as others
fit_power | Fit power-law distribution for an igraph

## -- G --

get_big_lay_nice | Layout with group nicely
get_community | Get community
get_e | Get edge information
get_group_skeleton | Get skeleton network according to a group
get_module | Get module
get_module_eigen | Get module_eigen
get_n | Get network information
get_v | Get vertex information
g_layout | Layout with group
g_layout_backbone | Layout with group nicely
g_layout_circlepack | Layout with group nicely
g_layout_multi_layer | Layout with group as a polygon
g_layout_nice | Layout with group nicely
g_layout_polyarc | Layout with group as a polygon
g_layout_polycircle | Layout with group as a polygon
g_layout_polygon | Layout with group as a polygon
g_layout_poly_sector | Layout with group
g_layout_stress | Layout with group nicely
g_layout_treemap | Layout with group nicely

## -- I --

input_cytoscape | Input a cyjs file exported by Cytoscape
input_gephi | Input a graphml file exported by Gephi
is.metanet | Is this object a metanet object?
is_metanet | Is this object a metanet object?

## -- L --

links_stat | Link summary of the network

## -- M --

metab | MetaNet networks abundance
metab_g | MetaNet networks metadata
micro | MetaNet networks abundance
micro_g | MetaNet networks metadata
module_detect | Detect the modules
module_eigen | Calculate the eigenvalue of each module and correlation of nodes and eigenvalue (node_eigen_cor).
module_expression | Calculate the eigenvalue of each module and correlation of nodes and eigenvalue (node_eigen_cor).
module_net | Generate a n-modules network
multi1 | MetaNet networks
multi_net_build | Multi-omics network build

## -- N --

nc | Calculate natural_connectivity
netD3plot | plot use networkD3
net_par | Calculate all topological indexes of a network

## -- O --

olympic_rings_net | Plot olympic rings using network

## -- P --

p.adjust.table | p.adjust apply on a correlation table (matrix or data.frame)
plot.cohesion | Cohesion calculation
plot.ggig | Plot a ggig
plot.metanet | Plot a metanet
plot.metanet_compare | Plot a metanet_compare
plot.rmt_res | Plot a rmt_res
plot.robust | Plot robust
plot.robustness | Plot robustness
plot.vulnerability | Plot vulnerability
plot_corr_heatmap | Plot a correlation heatmap
plot_e_type_bar | Plot e_type bar
plot_module_tree | Filter some modules as others
plot_multi_nets | Batch drawing multiple network diagrams
plot_net_degree | Plot degree distribution of networks
print.cohesion | Print method for 'cohesion' objects
print.coors | Print method for 'coors' objects
print.corr | Print method for 'corr' objects
print.ggig | Print method for 'ggig' objects
print.metanet | Print method for 'metanet' objects
print.metanet_compare | Print method for 'metanet_compare' objects
print.robust | Print method for 'robust' objects
print.robustness | Print method for 'robustness' objects
print.vulnerability | Print method for 'vulnerability' objects

## -- R --

rand_net | Degree distribution comparison with random network
rand_net_par | Net_pars of many random network
read_corr | Read a corr object
rmt | Get RMT threshold for a correlation matrix
RMT_threshold | Get RMT threshold for a correlation matrix
robustness | Evaluate the stability of a network
robust_test | Evaluate the stability of a network

## -- S --

save_corr | Save a corr object
show_MetaNet_logo | Show MetaNet logo
skeleton_plot | Get skeleton network according to a group
smallworldness | Calculate small-world coefficient
spatstat_layout | Generate spatial layout using 'spatstat'
summary.corr | Summary method for 'corr' objects
summary_module | Summary module index
summ_2col | Summaries two columns information

## -- T --

to_module_net | Transformation a network to a module network
transc | MetaNet networks abundance
transc_g | MetaNet networks metadata
transform_coors | Transform the layout of a 'coors' object
twocol_edgelist | Quick build a metanet from two columns table

## -- V --

venn_net | Venn network
vulnerability | Evaluate the stability of a network

## -- Z --

zp_analyse | Zi-Pi calculate
zp_plot | Zi-Pi calculate