pathfindR (version 1.4.2)

color_kegg_pathway: Color hsa KEGG pathway

Description

Color hsa KEGG pathway

Usage

color_kegg_pathway(
  pw_id,
  change_vec,
  normalize_vals = TRUE,
  node_cols = NULL,
  quiet = TRUE
)

Arguments

pw_id

hsa KEGG pathway id (e.g. hsa05012)

change_vec

vector of change values, names should be hsa KEGG gene ids

normalize_vals

should change values be normalized (default = TRUE)

node_cols

low, middle and high color values for coloring the pathway nodes (default = NULL). If node_cols=NULL, the low, middle and high color are set as "green", "gray" and "red". If all change values are 1e6 (in case no changes are supplied, this dummy value is assigned by input_processing), only one color ("#F38F18" if NULL) is used.

quiet

If TRUE, suppress status messages (if any), and the progress bar while downloading file(s)

Value

list containing:

1. file_path: path to colored hsa KEGG pathway diagram

2. all_key_cols: colors used for each change value bin

3. all_brks: breaks used for separating change values into bins

Examples

# NOT RUN {
   pw_id <- "hsa00010"
   change_vec <- c(-2, 4, 6)
   names(change_vec) <- c("hsa:2821", "hsa:226", "hsa:229")
   result <- pathfindR:::color_kegg_pathway(pw_id, change_vec)
# }