createDiagrammeRString: function to create a DiagrammeR string that can be used by...

In BenBruyneel/proteinDiscover: ProteinDiscover

function to create a DiagrammeR string that can be used by DiagrammeR::grViz() to plot a visual representation of the workflow

Description

function to create a DiagrammeR string that can be used by DiagrammeR::grViz() to plot a visual representation of the workflow

Usage

createDiagrammeRString(
  nodesTable,
  showBelow = TRUE,
  returnString = TRUE,
  hideDoubleParents = data.frame(name = c("Precursor Ions Quantifier", "Feature Mapper",
    "Reporter Ions Quantifier", "Protein Marker", "Peptide in Protein Annotation",
    "Modification Sites", "Peptide Isoform Grouper"), parent = c("last", "first", "last",
    "first", "first", "last", "first"))
)

Arguments

nodesTable	output from the nodeTable function. Columns that need to be present are node, name & parent
showBelow	boolean, default = TRUE. Set to FALSE when troubleshooting. Note that if set to FALSE, the parameter returnString will be ignored It is not recommended to depend on this parameter, as it will probably be removed in a newer version of the package
returnString	default = TRUE. Set to FALSE when troubleshooting. Note that the parameter showBelow makes it so that this parameter is ignored. It is not recommended to depend on this parameter, as it will probably be removed in a newer version of the package
hideDoubleParents	either NA (ignored) or a data.frame specifying what tp do in case of multiple parents. The data.frame should have the columns name and parent. The parent column should specify which parent to use ('first' or 'last') for connections

Value

character vector that can be passed on to DiagrammeR::grViz()

Note

during development it was noticed that some elements (nodes in the diagram) have more than one parent which is not seen in the proteome discoverer software of Thermo Scientific. The default data.frame 'corrects' known multiple parent nodes. If the parameter hideDoubleParents is set to NA, then the double parent connections are drawn.

an example of it's use: (workflowInfo(db))$nodeInfo$Consensus nodeTable() createDiagrammeRString() grViz()

BenBruyneel/proteinDiscover documentation built on March 16, 2024, 4:36 p.m.