MseekGraphs: MseekGraphs

In mjhelf/Metaboseek: Metaboseek platform

MseekGraphs

Description

setLayout(): change the graph layout of an existing MseekGraph object.

MseekGraph objects are igraph objects which have layout information and slots that are the same as MseekFT objects, except that the bulk of data is kept in an igraph object instead of a data.frame. These objects are read and displayed by the NetworkModule.

saveMseekGraph: save a MseekGraph object to a file, registering the save event in the processHistory if the format allows

loadMseekGraph: load a MseekGraph object from an .mskg or .graphml file (file extensions inform how file is loaded in)

simplify: simplify an MseekGraph object, reducing the number of edges using additional filters.

limitComponents: simplify an MseekGraph object, reducing the number of edges for any subgraph with more than n components.

Usage

## S4 method for signature 'MseekGraph'
setLayout(object, layoutFunction = "qgraph::qgraph.layout.fruchtermanreingold")

## S4 method for signature 'MseekFT'
buildMseekGraph(
  object,
  cosineThreshold = 0.6,
  layoutFunction = "qgraph::qgraph.layout.fruchtermanreingold"
)

## S4 method for signature 'MseekGraph'
saveMseekGraph(object, file, writeGraphML = FALSE, writeRDS = TRUE)

## S4 method for signature 'character'
loadMseekGraph(
  object,
  layoutFunction = "qgraph::qgraph.layout.fruchtermanreingold"
)

## S4 method for signature 'MseekGraph'
simplify(
  object,
  rankBy = NULL,
  maxK = 10,
  cosineThreshold = NULL,
  layoutFunction = "qgraph::qgraph.layout.fruchtermanreingold"
)

## S4 method for signature 'MseekGraph'
limitComponents(
  object,
  rankBy = "cosine",
  n = Inf,
  layoutFunction = "qgraph::qgraph.layout.fruchtermanreingold",
  percentile = TRUE
)

Arguments

object	an MseekGraph object (MseekFT for buildMseekGraph())
layoutFunction	function to use for layout of the resulting graph
cosineThreshold	if length > 0, will remove all edges with a cosine value below this
file	file path to write to
writeGraphML	write object to a .graphML file (will drop metadata and some columns)
writeRDS	write object to an .mskg (RDS) file; saves the entire object
rankBy	if length > 0, will use this edge attribute to iteratively remove the lowest scoring edges from the large clusters until
maxK	if length > 0, will only allow at most this many edges from each node
n	maximum number of nodes connected in a cluster
percentile	remove edges in percentile steps

Value

the MseekFT object, with saving event added to processHistory

mjhelf/Metaboseek documentation built on April 23, 2022, 12:09 p.m.