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MultIS (version 0.6.2)

lineplot_split_clone: Show line plots of all integration sites over time, split into facets by their respective clone.

Description

Show line plots of all integration sites over time, split into facets by their respective clone.

Usage

lineplot_split_clone(
  bd,
  rec,
  order = NULL,
  mapping = NULL,
  sim = NULL,
  silhouette_values = !is.null(sim),
  singletons = TRUE,
  zero_values = TRUE
)

Arguments

bd

The readouts of the integration sites over time.

rec

A matrix with columns "IS" and "Clone", that describes for each integration site, which clone it belongs to.

order

Integration site names will be converted to a factor. This allows to give the order for this factor, as it influences the order in which the lines are drawn.

mapping

A ggplot2 aesthetics mapping that will be merged with the aesthetics used by this plot.

sim

A similarity matrix giving the similarities for each pair of integration sites. Used if `silhouette_values` is `TRUE` to calculate the silhouette score.

silhouette_values

A boolean value that determines whether the silhouette values for each clone should be calculated and added to the facet labels. Requires `sim` to be present.

singletons

Whether to show clones that only have a single integration site.

zero_values

How to handle values that are zero. If `TRUE`, they remain zero and subsequently, a the measurement the line drops to zero. If `FALSE`, the values are removed and a gap in the line is shown.