R Script Visualization in Cytoscape

Displays the content of a R script into the 'Cytoscape' network-visualization app < https://cytoscape.org/>.

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

Edges of type sinewave represent the connection between a node and itself when used as an indice.

Edges of type dots represent the commands within a if, else, else if, ifelse or loop condition.