get_scaffold_map: Creates a Scaffold map

In ParkerICI/scgraphs: Analyzing single-cell data using graphs

Description

Creates a Scaffold map

Usage

get_scaffold_map(
  tab.clustered,
  col.names,
  tab.landmarks,
  G.landmarks = NULL,
  ew.influence = ceiling(length(col.names)/3),
  min.similarity = 0.5,
  inter.cluster.col.names = col.names,
  inter.cluster.weight.factor = 0.7,
  overlap.method = "repel"
)

Arguments

tab.clustered	A data.frame containing the clusters to be represented in the Scaffold map. Each row corresponds to a cluster, and each column to a different marker
col.names	A character vector of column names to be used for the analysis (these must correspond to the names of the columns in tab.clustered)
tab.landmarks	A data.frame containing the data corresponding to the landmark nodes. Each row corresponds to a landmark, and each column to a different cluster
G.landmarks	An igraph object represeting the identity and position of landmark nodes. If this is NULL the position of the landmark nodes will be calculated de-novo as part of the computation.
min.similarity	The minimum similarity value to be used as threshold to filter out edges. See the documentation for get_distances_from_landmarks
inter.cluster.col.names	A vector of column names to be used to calculate inter-cluster edges If this is NULL no inter-cluster edges will be present in the Scaffold map (not recommended)
inter.cluster.weight.factor	The weight of the inter-cluster edges will be multplied by this number before calculating the ForceAtlas2 layout. This can be used to fine tune the relative contribution of cluster-to-landmark vs cluster-to-cluster edges in the laytout
overlap.method	The method to be used for resolving nodes overlap in the final layout. See the documentation for complete_forceatlas2

Value

Returns a list with the following components

• G.landmarks: an igraph object representing the identity and position of landmark nodes, suitable for succesive invocations of this function

• G.complete: an igraph object representing the Scaffold map

ParkerICI/scgraphs documentation built on April 30, 2021, 1:10 p.m.