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