Man pages for MetaNet
Network Analysis for Omics Data
| adjacency_similarity | Calculate Similarity Between Two Graphs via Adjacency... |
| 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_arc | Layout as a arc |
| as_circle_tree | Layout as a circle_tree |
| as_coors | Transfer to a coors object |
| as.ggig | Transfer an igraph object to a ggig |
| 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 |
| 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 |
| 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... |
| c_net_compare | Compare Two Networks |
| c_net_difference | Difference two networks |
| c_net_ego | Extract ego-centric subnetwork with preserved class... |
| 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_intersect | Intersect two networks |
| 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 | 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... |
| Cohesion | Cohesion calculation |
| compare_rand | Net_pars of many random network |
| co_net | MetaNet networks |
| co_net2 | MetaNet networks |
| co_net_rmt | MetaNet networks |
| 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 | Filter some modules as others |
| fit_power | Fit power-law distribution for an igraph |
| 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_nice | Layout with group nicely |
| g_layout_polygon | Layout with group as a polygon |
| g_layout_poly_sector | Layout with group |
| grapes-less-than-greater-than-grapes | Assignment pipe |
| 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? |
| links_stat | Link summary of the network |
| metab | MetaNet networks abundance |
| metab_g | MetaNet networks metadata |
| MetaNet-package | MetaNet: Network Analysis for Omics Data |
| micro | MetaNet networks abundance |
| micro_g | MetaNet networks metadata |
| module_detect | Detect the modules |
| module_expression | Calculate the eigenvalue of each module and correlation of... |
| 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 | 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) |
| pipe | Pipe operator |
| plot_e_type_bar | Plot e_type bar |
| plot.ggig | Plot a ggig |
| plot.metanet | Plot a metanet |
| plot.metanet_compare | Plot a metanet_compare |
| plot_multi_nets | Batch drawing multiple network diagrams |
| plot_net_degree | Plot degree distribution of networks |
| 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.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 |
| rand_net | Degree distribution comparison with random network |
| read_corr | Read a corr object |
| RMT_threshold | Get RMT threshold for a correlation matrix |
| robustness | Plot robustness |
| robust_test | Plot robust |
| save_corr | Save a corr object |
| show_MetaNet_logo | Show MetaNet logo |
| smallworldness | Calculate small-world coefficient |
| spatstat_layout | Generate spatial layout using 'spatstat' |
| 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 |
| transform_coors | Transform the layout of a 'coors' object |
| twocol_edgelist | Quick build a metanet from two columns table |
| venn_net | Venn network |
| vulnerability | Plot vulnerability |
| zp_analyse | Zi-Pi calculate |
