Function reference • ParetoTI

All functions
`align_arc()` `gen_permut()`	Match/align arhetypes
`annotate_archetypes()`	Annotate archetypes with custom labels
`arch_dist()`	Compute distance to archetypes
`.archLines()`	add a line between all archetypes
`find_decreasing()` `fit_arc_gam_1()` `get_top_decreasing()` `find_decreasing_wilcox()` `bin_cells_by_arch()` `find_tradeoff_wilcox()`	Find features that are decreasing functions of distance from archetype
`find_gam_deriv()` `summary(<gam_deriv>)` `plot(<gam_deriv>)`	Find derivative of smooth curves from gam model fit (Generalised Additive Model, mgcv)
`find_set_activity_AUCell()` `find_set_activity_pseudoinv()`	Find activity of a gene set using AUCell model (continuos and binary)
`fit_logistic_model()` `plot_confusion()` `predict_logistic_prob()`	Classify cells with TensorFlow (logistic regression)
`fit_pch()` `k_fit_pch()` `fit_pch_bootstrap()` `average_pch_fits()` `fit_pch_resample()` `randomise_fit_pch()` `randomise_fit_pch1()` `fit_convhulln()` `merge_arch_dist()` `c(<k_pch_fit>)` `print(<pch_fit>)` `print(<k_pch_fit>)` `print(<b_pch_fit>)` `print(<r_pch_fit>)` `plot(<r_pch_fit>)` `plot_dim_var()` `pch_fit()` `subset.k_pch_fit()`	Find the smallest polytope (Principal Convex Hull) that contains most of the data
`generate_arc()` `generate_data()`	Generate random data within specified archetypes
`geo_sketch()`	Create downsampled representation of the data with Geometric Sketch
`hello()`	Hello, World!
`install_py_pcha()`	Install python module py_pcha and numpy
`map_gene_annot()`	Convert gene identifiers with AnnotationHub
`map_go_annot()` `filter_go_annot()` `measure_activity()` `load_go_ontology()` `map_gwas_annot()` `map_promoter_tf()`	Annotate genes with GO terms and measure their activities
`paa_poisson()`	Create probabilistic archetypal analysis model in greta (tensorflow backend)
`plot_arc()` `arch_to_tsne()` `arch_to_umap()`	Plot data with archetypes in 2D, 3D and a panel of 2D
`plot_arc_var()`	Plot variance in positions, t-ratios and variance explained by polytope fit
`plot_arch_struct()`	Find and plot similarity structure between archetypes
`plot_gam()`	Plot gam model fit for multiple genes and archetypes (Generalised Additive Model, mgcv)
`compute_gene_deviance()` `poisson_regression()`	Poisson regression model to find effects of sample covariates on variables
`build_logit_vert()` `make_features()` `predict_vert()` `split_train_val()` `plot_confusion_vert()` `get_feature_weights()`	Logistic regression model to classify vertices
`project_to_pcs()` `project_from_pc()`	Project archetypes and data in PCA dimentions
`rand_var()`	Permute each column of a matrix by sampling from empirical distribution

Reference

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