weighted_spring_model: Plot the relationship of integration sites as a graph.

In MultIS: Reconstruction of Clones from Integration Site Readouts and Visualization

Description

Integration sites will be represented as nodes in the graph, while their mutual similarity is indicated by the line size and opaqueness of the lines between them.

Usage

weighted_spring_model(
  readouts,
  mapping,
  gt,
  sim = get_similarity_matrix(readouts, self = NA, upper = FALSE, parallel = FALSE),
  rec_pal = NULL,
  clone_pal = NULL,
  line_color = "#009900FF",
  seed = 4711L
)

Arguments

readouts	The integration site readouts that this spring model is based on.
mapping	The reconstructed mapping from clones to integration sites. This is represented as a matrix with two columns "IS" and "Clone".
gt	The ground truth mapping from clones to integration sites, if available. Same structure as 'mapping'.
sim	The similarity matrix holding the similarities between all integration sites.
rec_pal	A named vector color palette holding colors for each integration site. Will be used as the fill color for the nodes.
clone_pal	A named vector color palette holding colors for each integration site. Will be used as the line color for the nodes.
line_color	The line color to use for the edges of the graph.
seed	A seed that will be set using 'set.seed()' to ensure consistent behaviour with the layout that is provided by 'igraph'.

Value

A ggplot object that contains the generated graph.

MultIS documentation built on Aug. 6, 2021, 5:07 p.m.