Analyzing and visualizing KEGG information using the grammar of
graphics
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Documentation for package ‘ggkegg’ version 1.2.3
Help Pages
| add_title | addTitle |
| append_cp | append_cp |
| append_label_position | append_label_position |
| assign_deseq2 | assign_deseq2 |
| carrow | carrow |
| combine_with_bnlearn | combine_with_bnlearn |
| convert_id | convert_id |
| create_test_module | create_test_module |
| create_test_network | create_test_network |
| create_test_pathway | create_test_pathway |
| edge_matrix | edge_matrix |
| edge_numeric | edge_numeric |
| edge_numeric_sum | edge_numeric_sum |
| geom_kegg | geom_kegg |
| geom_node_rect | geom_node_rect |
| geom_node_rect_kegg | geom_node_rect_kegg |
| geom_node_rect_multi | geom_node_rect_multi |
| geom_node_shadowtext | geom_node_shadowtext |
| get_module_attribute | get_module_attribute |
| get_module_attribute-method | get_module_attribute |
| get_network_attribute | get_network_attribute |
| get_network_attribute-method | get_network_attribute |
| ggkegg | ggkegg |
| ggkeggsave | ggkeggsave |
| ggplot_add.geom_kegg | ggplot_add.geom_kegg |
| ggplot_add.geom_node_rect_kegg | ggplot_add.geom_node_rect_kegg |
| ggplot_add.geom_node_rect_multi | ggplot_add.geom_node_rect_multi |
| ggplot_add.overlay_raw_map | ggplot_add.overlay_raw_map |
| ggplot_add.stamp | ggplot_add.stamp |
| highlight_entities | highlight_entities |
| highlight_module | highlight_module |
| highlight_set_edges | highlight_set_edges |
| highlight_set_nodes | highlight_set_nodes |
| module | module KEGG module parsing function |
| module_abundance | module_abundance weighted mean abundance of fraction of present KO in the block |
| module_completeness | module_completeness |
| module_text | module_text Obtain textual representation of module definition for all the blocks |
| multi_pathway_native | multi_pathway_native |
| network | KEGG network parsing function |
| network_graph | network_graph |
| node_matrix | node_matrix |
| node_numeric | node_numeric |
| obtain_sequential_module_definition | obtain_sequential_module_definition |
| output_overlay_image | output_overlay_image |
| overlay_raw_map | overlay_raw_map |
| pathway | pathway |
| pathway_abundance | pathway_abundance |
| pathway_info | pathway_info |
| plot_kegg_network | plot_kegg_network |
| plot_module_blocks | plot_module_blocks |
| plot_module_text | plot_module_text |
| process_line | process_line |
| process_reaction | process_reaction |
| rawMap | rawMap |
| rawValue | rawValue |
| return_line_compounds | return_line_compounds |
| stamp | stamp |