Reference

All functions

Kinetic functions

fit_genotype_ccm()

Fits a cell count model (CCM) for a given genotype using a specified dataset of cell counts (CCS).

fit_wt_model()

Fits a wild type (WT) model to a cell dataset (CDS) by estimating cell count dynamics over time and accounting for nuisance variables.

fit_mt_models()

Fits models for analyzing multi-timepoint perturbation data using a cell dataset (cds).

plot_cell_type_control_kinetics()

Generates a kinetic plot of cell type control data over time.

plot_cell_type_perturb_kinetics()

Generates a plot to visualize the kinetics of cell type perturbations over time.

Graph functions

new_cell_state_graph()

Creates a new cell state graph object from an input graph and a cell count set.

assemble_partition()

Assembles a partition for a given cell dataset (CDS) by fitting wild-type (WT) and mutant (MT) models, constructing state transition graphs, and assessing perturbation effects.

Plotting functions

plot_annotations()

Generates a plot of cell state graphs with various customization options.

plot_gene_expr()

Plots gene expression data on a cell state graph.

plot_abundance_changes()

Generates a plot to visualize changes in cell state abundances.

plot_degs()

Plots differentially expressed genes (DEGs) on a cell state graph, with customizable appearance and layout options.