KEGG pathway visualization by ggplot2


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Documentation for package ‘ggkegg’ version 1.2.1

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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