plot_pathways_w_sampling: Plot most probable pathways before a sampling event computed...

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

Plot most probable pathways before a sampling event computed from a Mutual Hazard Network

Description

This function takes a Mutual Hazard Network as input and plot the most probable mutational pathways before a sampling event.

Usage

plot_pathways_w_sampling(
  Theta,
  mutations,
  top_M = 10,
  lambda_s = 1,
  mutation_colors = NULL,
  prob_digits = 2,
  full = FALSE
)

Arguments

Theta	An n-by-n matrix representing a Mutual Hazard Network.
mutations	A list of mutation names, which must be unique values. If no names are given, then the mutation IDs will be used.
top_M	Number of most probable 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)
full	A boolean flag indicating whether the full MHN is used. If false, then only mutations with non-zero off-diagonal entries will be used (default: FALSE).

Author(s)

Xiang Ge Luo

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