plot_observed_pathways: Plot most frequent observed pathways from a cohort of...

In cbg-ethz/TreeMHN: Joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity from single-cell mutation trees

Plot most frequent observed pathways from a cohort of mutation trees

Description

This function takes a cohort of mutation trees and the estimated Mutual Hazard Network as input and plot the most frequent observed pathways.

Usage

plot_observed_pathways(
  tree_obj,
  Theta,
  top_M = 10,
  lambda_s = 1,
  mutation_colors = NULL,
  prob_digits = 2,
  at_least_twice = TRUE
)

Arguments

tree_obj	A TreeMHN object.
Theta	An n-by-n matrix representing a Mutual Hazard Network.
top_M	Number of most frequent pathways to plot (Default: 10).
lambda_s	Sampling rate (Default: 1)
mutation_colors	A named vector with the color codes for all mutations (Default: NULL)
prob_digits	Number of digits to show for the probabilities (Default: 2)
at_least_twice	A boolean flag indicating whether only trajectories that appear at least twice in the dataset are shown (Default: TRUE). If true, this flag will overwrite the top_M argument.

Author(s)

Xiang Ge Luo

cbg-ethz/TreeMHN documentation built on Jan. 29, 2024, 1:29 p.m.