KEGG_lincs {KEGGlincs} | R Documentation

## Combines all other package functions for one-step pathway visualization

### 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)

[Package KEGGlincs version 1.8.0 Index]