Package index • MetaNet

All functions
`Cohesion()` `plot(<cohesion>)`	Cohesion calculation
`RMT_threshold()` `rmt()`	Get RMT threshold for a correlation matrix
`anno_edge()`	Use dataframe to annotate edges of an igraph
`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_arc()`	Layout as a arc
`as_circle_tree()`	Layout as a circle_tree
`as_line()`	Layout as a line
`as_polyarc()`	Layout as a polyarc
`as_polycircle()`	Layout as a polycircle
`as_polygon()`	Layout as a polygon
`c_net_annotate()`	Annotate a metanet
`c_net_build()`	Construct a metanet from a corr object
`c_net_calculate()`	Calculate correlation for one or two t(otutab), or distance for one t(otutab).
`c_net_filter()`	Filter a network according to some attributes
`c_net_from_edgelist()`	Construct a network from edge_list dataframe
`c_net_layout()`	Layout coordinates
`c_net_load()`	Load network file
`c_net_plot()`	Plot a metanet
`c_net_save()`	Save network file
`c_net_set()`	Set basic attributes from totu table
`c_net_stability()` `robust_test()` `vulnerability()` `robustness()`	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
`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
`co_net`	MetaNet networks
`co_net2`	MetaNet networks
`co_net_rmt`	MetaNet networks
`rand_net_par()` `compare_rand()`	Net_pars of many random network
`df2net_tree()`	Transform a dataframe to a network edgelist.
`extract_sample_net()`	Extract each sample network from the whole network
`fast_cor()`	Fast correlation calculation
`filter_n_module()` `combine_n_module()` `plot_module_tree()`	Filter some modules as others
`fit_power()`	Fit power-law distribution for an igraph
`g_layout()`	Layout with group
`g_layout_nice()` `g_layout_circlepack()` `g_layout_treemap()` `g_layout_backbone()` `g_layout_stress()`	Layout with group nicely
`g_layout_polygon()` `g_layout_polyarc()` `g_layout_polycircle()`	Layout with group as a polygon
`get_community()`	Get community
`get_e()`	Get edge information
`get_group_skeleton()` `skeleton_plot()`	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
`input_gephi()`	Input a graphml file exported by Gephi
`is_metanet()`	Is this object a metanet object?
`links_stat()`	Link summary of the network
`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()` `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
`nc()`	Calculate natural_connectivity
`netD3plot()`	plot use networkD3
`net_par()` `c_net_index()`	Calculate all topological indexes of a network
`olympic_rings_net()`	Plot olympic rings using network
`p.adjust.table()`	p.adjust apply on a correlation table (matrix or data.frame)
`plot(<ggig>)`	Plot a ggig
`plot(<metanet>)`	Plot a metanet
`plot(<rmt_res>)`	Plot a rmt_res
`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(<robust>)`	Print method for 'robust' objects
`print(<robustness>)`	Print method for 'robustness' objects
`print(<vulnerability>)`	Print method for 'vulnerability' objects
`rand_net()`	Degree distribution comparison with random network
`read_corr()`	Read a corr object
`plot(<robust>)`	Plot robust
`plot(<robustness>)`	Plot robustness
`save_corr()`	Save a corr object
`show_MetaNet_logo()`	Show MetaNet logo
`smallworldness()`	Calculate small-world coefficient
`summ_2col()`	Summaries two columns information
`summary(<corr>)`	Summary method for 'corr' objects
`summary_module()`	Summary module index
`to_module_net()`	Transformation a network to a module network
`transc`	MetaNet networks abundance
`transc_g`	MetaNet networks metadata
`twocol_edgelist()`	Quick build a metanet from two columns table
`venn_net()`	Venn network
`plot(<vulnerability>)`	Plot vulnerability
`zp_analyse()` `zp_plot()`	Zi-Pi calculate

Reference

All functions