KEGG_lincs: Combines all other package functions for one-step pathway...

In shanawhite-UC/KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data

Description

Combines all other package functions for one-step pathway visualization

Usage

KEGG_lincs(pathwayid, cell_line = NA, refine_by_cell_line = NA,
  add_L1000_edge_data = TRUE, significance_markup = TRUE,
  data_type = "100_full", pert_time = 96, only_mapped = TRUE,
  layered_nodes = FALSE, graph_title = "default", get_data = FALSE,
  convert_KEGG_IDs = TRUE, tidy_edge = FALSE)

Arguments

pathwayid	A KEGG pathway ID of the form "hsa12345" (only human pathways currently)
cell_line	If left as NA will generate a pathway map without data-dependent attributes (such as edge width). To use in combination with LINCS data, choose from the set of cell lines: (A375,A549,ASC,HA1E,HCC515,HEK293T,HEKTE,HEPG2,HT29,MCF7,NCIH716,NPC,PC3, SHSY5Y,SKL,SW480,VCAP)
refine_by_cell_line	A logical indicator
add_L1000_edge_data	A logical indicator
significance_markup	A logical indicator; if set to TRUE will color edges based on direction and significance of correlation (as determined by user-data-analysis)
data_type	Choose from data types: (100_full, 100_bing, 50_lm)
pert_time	Choose from (6,24,48,96,120,144,168)
only_mapped	A logical indicator; if set to FALSE will return 'de-novo' edges that 'exist' in data but are not documented in KEGG
layered_nodes	A logical indicator; if set to TRUE will create a graph with 'stacked' nodes that the user can manipulate when multiple nodes are mapped to one location
graph_title	An optional user-specified graph title
get_data	A logical indicator; if set to true, will return the 'expanded' edge information for the specified pathway
convert_KEGG_IDs	A logical indicator; if set to TRUE KEGG compounds will remain labeled via KEGG codes (do not need KEGGREST)
tidy_edge	A logical indicator; must be set to FALSE for expanded edges

Value

A dynamic map in Cytoscape automatically formatted for convenient viewing and, if idicated by user, a data.frame object with detailed information for 'expanded' KEGG edges

Examples

## Not run:  

#Default KEGG pathway with colored edges representing type of relationship:
KEGG_lincs("hsa04115", convert_KEGG_IDs = FALSE)

#KEGG pathway with edge width and color based on observed experimental data:
KEGG_lincs("hsa04115", "HA1E")

#Have edge information data.frame to be output to the global environment:
p53_edge_info <- KEGG_lincs("hsa04115", graph_title = "p53"
                             convert_KEGG_IDs = FALSE, get_data = TRUE)
                             
## End(Not run)

shanawhite-UC/KEGGlincs documentation built on May 29, 2019, 8:07 p.m.