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_pkgdown.yml
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/
_pkgdown.yml
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destination: docs
template:
bootstrap: 5
url: caravagnalab.github.io/lineaGT
reference:
- title: Data
desc: Example of the input datasets and of the fitted object.
contents:
- cov.df.example
- vaf.df.example
- x.example
- title: Fit function
desc: Main function to perform the fit of the model.
contents:
- fit
- fit_mutations
- fit_phylogenies
- fit_growth_rates
- filter_dataset
- title: Getter functions
desc: Functions to extract the main elements of the fitted object.
contents:
- get_lineages
- get_dimensions
- get_timepoints
- get_cov_dataframe
- get_vaf_dataframe
- get_labels
- get_unique_labels
- get_unique_muts_labels
- get_mean
- get_sigma
- get_covariance_Sigma
- get_covariance_Cholesky
- get_weights
- get_z_probs
- get_ISs
- estimate_n_pops
- title: Visualization functions
desc: Functions to visualize the fit results.
contents:
- plot_scatter_density
- plot_mixture_weights
- plot_marginal
- plot_mullerplot
- plot_growth_regression
- plot_growth_rates
- plot_vaf
- plot_vaf_time
- plot_phylogeny
- plot_differentiation_tree
- title: Training
desc: Functions to visualize losses, Information Criteria and gradient norms computed during training.
contents:
- plot_losses
- plot_IC
- plot_gradient_norms
- title: S3 object methods
desc: Print and plot methods for the fitted object.
contents:
- print.mvnmm
- plot.mvnmm
- title: Helper functions
desc: Function to configure and install the required dependencies.
contents:
- configure_environment
- have_loaded_env
- have_python_deps
- which_conda_env
- load_conda_env