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_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.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 |