# Analyzing and visualizing KEGG information using the grammar of graphics

## Documentation for package ‘ggkegg’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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