createColumnFilter: Create Column Filter

In cytoscape/RCy3: Functions to Access and Control Cytoscape

Create Column Filter

Description

Creates a filter to control node or edge selection. Works on columns of boolean, string, numeric and lists. Note the unique restrictions for criterion and predicate depending on the type of column being filtered.

Usage

createColumnFilter(
  filter.name,
  column,
  criterion,
  predicate,
  caseSensitive = FALSE,
  anyMatch = TRUE,
  type = "nodes",
  hide = FALSE,
  network = NULL,
  base.url = .defaultBaseUrl,
  apply = TRUE
)

Arguments

filter.name	Name for filter.
column	Table column to base filter upon.
criterion	For boolean columns: TRUE or FALSE. For string columns: a string value, e.g., "hello". If the predicate is REGEX then this can be a regular expression as accepted by the Java Pattern class (https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html). For numeric columns: If the predicate is BETWEEN or IS_NOT_BETWEEN then this is a two-element vector of numbers, example: c(1,5), otherwise a single number.
predicate	For boolean columns: IS, IS_NOT. For string columns: IS, IS_NOT, CONTAINS, DOES_NOT_CONTAIN, REGEX. For numeric columns: IS, IS_NOT, GREATER_THAN, GREATER_THAN_OR_EQUAL, LESS_THAN, LESS_THAN_OR_EQUAL, BETWEEN, IS_NOT_BETWEEN
caseSensitive	(optional) If string matching should be case sensitive. Default is FALSE.
anyMatch	(optional) Only applies to List columns. If true then at least one element in the list must pass the filter, if false then all the elements in the list must pass the filter. Default is TRUE.
type	(optional) Apply filter to "nodes" (default) or "edges".
hide	Whether to hide filtered out nodes and edges. Default is FALSE. Ignored if all nodes or edges are filtered out. This is an alternative to filtering for node and edge selection.
network	(optional) Name or SUID of the network. Default is the "current" network active in Cytoscape.
base.url	(optional) Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://localhost:1234 and the latest version of the CyREST API supported by this version of RCy3.
apply	(bool) True to execute filter immediately (default); False to define filter but not execute it (available in Cytoscape 3.9+).

Value

List of selected nodes and edges.

Examples

createColumnFilter('myFilter', 'log2FC', c(-1,1), "IS_NOT_BETWEEN")
createColumnFilter('myFilter', 'pValue', 0.05, "LESS_THAN")
createColumnFilter('myFilter', 'function', "kinase", "CONTAINS", FALSE)
createColumnFilter('myFilter', 'name', "^Y.*C$", "REGEX")
createColumnFilter('myFilter', 'isTarget', TRUE , "IS", apply=FALSE)
createColumnFilter('myFilter', 'isTarget', TRUE , "IS", hide=TRUE)

cytoscape/RCy3 documentation built on Nov. 1, 2024, 2:49 a.m.