R Script Visualization in Cytoscape.
ScriptMapR
R Script Visualization in Cytoscape
This function allows the user to represent the content of a given script in 'Cytoscape' (https://cytoscape.org/). Therefore it is required to have a functioning version of 'Cytoscape' 3.6.1 or greater.
Each variable is represented as a node and edges represent commands that call the variable.
User defined functions are represented and pooled as a group, collapsed and extracted to a subnetwork to avoid latency.
Color coding
Nodes
A color code is associated to each nodes:
white: intermediate variables (that are created and used to create new ones),
pink: subsets of a variable (ex: var2 in var1$var2),
green: final variables (that are created and not used afterwards),
red: warnings, message and stop functions,
yellow: if, else if, else and ifelse functions,
orange: for, foreach and while functions,
blue: *print, cat or other functions at beginning of line,
gray: packages import and session info (wd)
Edges
Edge color reports the sequence of command on a blue scale
- light blue: early in the script
- dark blue: late in the script
Node color code extend to edges in case of loops or tests
- Orange edge bypass: commands within for loop
- Yellow edge bypass: commands within if, else, else if, ifelse