createList: createList

In Director: A dynamic visualization tool of multi-level data

Description

Take a subset of the input data frame or matrix corresponding to the required Sankey values.

Usage

createList(inputList, inputFC = NULL, node = "genes", fc = "foldChange",
  source = "source", target = "target", description = "description",
  value = "value", sourcefc = "sourcefc", targetfc = "targetfc")

Arguments

inputList	Data frame or matrix containing the necessary parameters described below.
inputFC	Data frame or matrix containing node names (source and target) and corresponding quantitative values. If this input is defined, then input-specific parameters 'node' and 'fc' should be defined. Inputs 'source', 'target', 'description' and 'value' are still referenced from inputList.
node	Column name of inputFC containing names to display of source and target nodes. Paths defined in inputList identify which nodes are sources and which are targets.
fc	Column name of inputFC containing quantitative values representing the nodes.
source	Column name of inputList containing names to display of starting nodes. Paths are drawn from these points to their corresponding target nodes.
target	Column name of inputList containing names to display of destination nodes. Paths are drawn to these point from their corresponding source nodes.
description	Optional column name of inputList containing additional information about connection, e.g. the gene name of a transcript target node, or family name of related target genes.
value	Column name of inputList containing quantitative values representing the relationship between sources and targets.
sourcefc	Column name of inputList containing quantitative values representing the sources.
targetfc	Column name of inputList containing quantitative values representing the targets.

Value

a data.frame List

Examples

nodevals <- runif(5,-2,2)
tempList <- data.frame(source=c("A","B","C","D"),
    target=c("C","D","E","E"),
    addedInfo=c("c","d","vowel","vowel"),
    relationValue=runif(4,-1,1),
    sourceValue=nodevals[1:4],
    targetValue=nodevals[c(3,4,5,5)])
tempFC <- data.frame(genes=c("A","B","C","D","E"), foldChange=runif(5,-2,2))
# inputList only
createList(tempList, description="addedInfo", value="relationValue", 
sourcefc="sourceValue", targetfc="targetValue")
# inputList and inputFC
createList(tempList, tempFC, value="relationValue",sourcefc="sourceValue",
targetfc="targetValue")

Director documentation built on Nov. 8, 2020, 5:55 p.m.