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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.