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,kegg_module-method
                        get_module_attribute
get_network_attribute   get_network_attribute
get_network_attribute,kegg_network-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
