set_parents: Set parents for samples

In jellyfisher: Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots

Set parents for samples

Description

Given a list of jellyfish input tables and a named list of parents for each sample, set the parent for each sample.

Usage

set_parents(tables, parents, unset_missing = FALSE)

Arguments

tables	A list of tables (samples, phylogeny, compositions, ranks)
parents	A named list of parents for each sample. Keys are the samples and values are their new parents
unset_missing	If TRUE, unset the parent for samples that are not in the parent list

Details

By default, all samples that have no explicit parent are children of the inferred root sample. You can customize the parent-child relationships by modifying the parent column in the samples data frame before plotting.

You can also modify the relationships using the set_parents function.

For example, if you have three samples, A, B, and C, they will have the following relationships by default:

    Root
   / | \
  A  B  C

With the explicit parents, you can customize the relationships:

tables |>
  set_parents(list(
    # The parent of C is B
    C = "B"
  ) |>
  jellyfisher()

    Root
   /  \
  A    B
        \
         C

Value

A list of tables with parents set for each sample

Examples

jellyfisher_example_tables |>
  select_patients("EOC809") |>
  set_parents(list("EOC809_r1Bow1_DNA1" = "EOC809_p2Per1_cO_DNA2")) |>
  jellyfisher()

jellyfisher documentation built on April 4, 2025, 1:41 a.m.