Man pages for vanhasseltlab/IMatlas
a tool for design and interpretation of metabolomics studies in immunology
| add_centrality | Add centrality to your graph |
| add_gos | Assign Gene Ontologies to vertices |
| add_layout | Calculate layout for nodes in graph |
| add_metadata | Adding metadata to igraph object |
| add_node_pvalues | calculate all node-based pvalues |
| add_node_types | Add the type of each node |
| add_precision | add precision score to node |
| add_vertice_colors | Adding colors to vertices of the graph |
| adjust_folder | adjust folder path in given options |
| example_graph | Produce the example graph |
| filter_metabolites | Filter metabolites |
| get_2d_scatter | Produce 2D pvalue-closeness scatter plot |
| get_go_ids | Get Gene Ontology identifiers by name |
| get_go_names | get Gene Ontology names |
| get_graph | Get igraph object |
| get_graph_summary | Get a summary of the graph |
| get_metabolite_ids | Get metabolite identifiers |
| get_metabolite_metadata | Get metadata of metabolites |
| get_metabolite_names | Get metabolite names |
| get_node_summary | Get a summary of all nodes in a graph |
| get_process_summary | Get a summary of a process graph |
| get_protein_ids | Retrieve protein identifiers using names |
| get_protein_names | Retrieve protein names using identifiers |
| get_proteins_by_go | Return all proteins associated with a GO |
| get_proteins_by_goid | Get protein names by Gene Ontology identifiers |
| load_data | Load Data |
| metabolic_process_summary | Return a long-format DataFrame with GO-Pvalue combinations... |
| metabolite_go_graph | Construct a network of metabolites and GOs |
| na_omit_list | Remove NAs from Lists |
| remove_unconnected | Remove unconnected nodes |
| run_preprocessing | Run Preprocessing |
| run_shiny | Run Shiny App |
| run_textmining | Run the text mining |
| to_plotly | Convert igraph object to an interactive Plotly |
