Attribute Formulas

As of Cytoscape 2.8, attribute values may be formulas. A typical example is =ABS($otherAttrib + LOG(10.2)). Formulas are modelled after Excel™ but only support references to other attributes at the same node, edge or network. Since Cytoscape attribute names may contain embedded spaces, optional braces around the attribute name (required if the name is not simply a letter followed by one or more letters or digits) is allowed e.g. ${a name with spaces}. Backslashes, opening braces and dollar signs in attribute names have to be escaped with a leading backslash. For example the attribute name ex$am{p\le would have to be written as ${ex\$am\{p\\le}. Currently supported operators are the four basic arithmetic operators and the ^ exponentiation operator. +, -, *, and \ are left-associative and ^ is right-associative. The string concatenation operator is & and string constants are written with double-quotes ". In order to embed a double-quote or a backslash in a string they have to be escaped with a leading backslash, therefore the string "\ must be written as "\"\\". Formula results must be compatible with the type of the attribute that they have been assigned to. The rules are rather lax though, for example anything can be interpreted as a string and all numeric values will be accepted for a boolean (or logical) attribute where non-zero will be interpreted as true and zero as false. For integer attributes floating point values will be converted using the rules of the Excel™ INT function.

Supported Functions

Currently we support the following functions:

Numeric Functions

String Functions

Logical/Boolean Functions

Miscellaneous Functions