summary: RCX and aspect summary

In frankkramer-lab/RCX: R package implementing the Cytoscape Exchange (CX) format

RCX and aspect summary

Description

summary is a generic function used to produce result summaries of the RCX object. The function invokes particular methods which depend on the class of the first argument.

Usage

## S3 method for class 'RCX'
summary(object, ...)

## S3 method for class 'MetaDataAspect'
summary(object, ...)

## S3 method for class 'NodesAspect'
summary(object, ...)

## S3 method for class 'EdgesAspect'
summary(object, ...)

## S3 method for class 'NodeAttributesAspect'
summary(object, ...)

## S3 method for class 'EdgeAttributesAspect'
summary(object, ...)

## S3 method for class 'NetworkAttributesAspect'
summary(object, ...)

## S3 method for class 'CartesianLayoutAspect'
summary(object, ...)

## S3 method for class 'CyGroupsAspect'
summary(object, ...)

## S3 method for class 'CyHiddenAttributesAspect'
summary(object, ...)

## S3 method for class 'CyNetworkRelationsAspect'
summary(object, ...)

## S3 method for class 'CySubNetworksAspect'
summary(object, ...)

## S3 method for class 'CyTableColumnAspect'
summary(object, ...)

## S3 method for class 'CyVisualPropertiesAspect'
summary(object, ...)

## S3 method for class 'CyVisualProperty'
summary(object, ...)

## S3 method for class 'AspectIdColumn'
summary(object, ...)

## S3 method for class 'AspectRefColumn'
summary(object, ...)

## S3 method for class 'AspectReqRefColumn'
summary(object, ...)

## S3 method for class 'AspectValueColumn'
summary(object, ...)

## S3 method for class 'AspectAttributeColumn'
summary(object, ...)

## S3 method for class 'AspectListLengthColumn'
summary(object, ...)

Arguments

object	an object; RCX object or aspect (or column of data.frame)
...	additional arguments affecting the summary produced.

Details

The form of the returned summary depends on the class of its argument, therefore it is possible to summarize RCX objects and their single aspects.

To enhance readability of the summary, some additional classes have summary functions, that are used to show for example ids of an aspect, required and optional references to ids of aspects, or the number of elements in lists.

Value

object summary as list

Methods (by class)

• AspectIdColumn: Summarize an id property

• AspectRefColumn: Summarize an optional property, that references the ids of an other aspect

• AspectReqRefColumn: Summarize a required property, that references the ids of an other aspect

• AspectValueColumn: Summarize the occurrences of the different elements in the property

• AspectAttributeColumn: Summarize the different attributes in the property

• AspectListLengthColumn: The property is a list of vectors, so summarize the length of the vectors

Examples

rcx = createRCX(
  nodes = createNodes(name = c("a","b","c")),
  edges = createEdges(source=1, target=2)
)

summary(rcx)

frankkramer-lab/RCX documentation built on Feb. 4, 2023, 5:12 p.m.