createList {Director} | R Documentation |
Take a subset of the input data frame or matrix corresponding to the required Sankey values.
createList(inputList, inputFC = NULL, node = "genes", fc = "foldChange", source = "source", target = "target", description = "description", value = "value", sourcefc = "sourcefc", targetfc = "targetfc")
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. |
a data.frame List
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")