## Cohort functions

These functions can be used to create or modify a REVOLVER cohort and its trees.

revolver_cohort()

Construct a REVOLVER cohort.

revolver_check_cohort()

Check basic inconsistencies in a REVOLVER cohort.

compute_clone_trees()

Compute CCF-based clone trees for a patient (phylogenies).

input_custom_trees()

Add a custom set of trees for a patient.

CCF_parser()

Parser function for the required CCF input field.

remove_drivers()

Remove a list of driver events from the cohort.

remove_patients()

Remove patients from the cohort.

## Analysis functions

These functions can be used to analyse a REVOLVER cohort.

revolver_fit()

Fit a REVOLVER model.

revolver_cluster()

Compute hierarchical clustering for a REVOLVER cohort.

revolver_jackknife()

Compute clusters stability via the jackknife.

## Getters functions

These functions can be used to extract data from a REVOLVER cohort object. These include the raw data used to create the cohort, driver information, clonal and subclonal events, the trees that are associated to the patients and other analysis results.

Data()

Extract all data for a patient.

Drivers()

Extract driver data for a patient.

Truncal()

Extract clonal (i.e., truncal) data for a patient.

Subclonal()

Extract subclonal data for a patient.

Samples()

Extract all samples ids for a patient.

Clonal_cluster()

Extract the clonal cluster id for a patient.

CCF()

Extract all CCF or binary data for a patient.

CCF_clusters()

Extract all clusters in the data of a patient.

Phylo()

Extract the trees available for a patient.

ITransfer()

Extract the information transfer available for a patient.

get_features()

Return summary features for the cohort.

Cluster()

Get REVOLVER clusters information for this cohort

Jackknife_patient_coclustering()

Get jackknifed patient co-clustering probability.

Jackknife_cluster_stability()

Get jackknifed cluster stability.

Jackknife_trajectories_stability()

Get jackknifed trajectories stability.

## Stats functions

These functions can be used to extract either cohort-level statistics data from a REVOLVER cohort object, and other statistics that regard the computations performed on the cohort.

Stats()

Summary statistics for the cohort's patients.

Stats_cohort()

Synonim for function Stats.

Stats_drivers()

Summary statistics for the cohort's driver events.

Stats_fits()

Summary statistics for the cohort's fits.

Stats_trees()

Summary statistics for the cohort's trees.

DET_index()

Compute the index of Divergent Evolutionary Trajectories.

## Plotting functions

These functions can be used to plot data, fits and clusters from a REVOLVER cohort object.

plot_DET_index()

Plot the index of Divergent Evolutionary Trajectories.

plot_clusters()

Plot the heatmaps of REVOLVER"s clusters.

plot_dendrogram()

Plot the dendrogram of REVOLVER"s clusters.

plot_drivers_clonality()

Plot the clonality status of cohort driver events.

plot_drivers_graph()

Plot graph-alike summary statistics for the cohort drivers.

plot_drivers_occurrence()

Plot the occurrence of drivers across the cohort.

plot_jackknife_cluster_stability()

Plot the patients' jackknife cluster staability

plot_jackknife_coclustering()

Plot the patients' jackknife co-clustering probability

plot_jackknife_trajectories_stability()

Plot the patients' jackknife trajectory frequencies.

plot_patient_CCF_histogram()

Plot the data histogram for a patient.

plot_patient_data()

Plot the data for a patient.

plot_patient_mutation_burden()

Plot the mutation burden for a patient.

plot_patient_oncoprint()

Plot the oncoprint for a patient.

plot_patient_trees()

Plot REVOLVER trees for a patient.

plot_patient_trees_scores()

Plot the scores for a patient's trees.

plot_penalty()

Plot the fit penalty.

distinct_palette_few()

Palette of few distinct colours.

distinct_palette_many()

Palette of n distinct colours.

gradient_palette()

## S3 functions

The two S3 classes of REVOLVER objects implement the following S3 mehtods. Class rev_cohort represents a basic cohort object before the fits, class rev_cohort_fit is a cohort object where fits are now available.

print(<rev_cohort>)

Summary print of a cohort.

print(<rev_cohort_fit>)

Summary print of a cohort with fits.

plot(<rev_cohort>)

Summary scatterplot of a cohort.

plot(<rev_cohort_fit>)

Summary scatterplot of a cohort's fits.