CardamomOT.tools.plot_results_sim

Plotting utilities for comparing data, mixture, trajectories, and simulations.

Functions

plot_results_rna_mixture(split, p[, project_on_full, ...])

Compare observed data to the NB mixture fit (UMAP by time and cell type).

plot_results_rna_clean(p[, stim, prior, ...])

Compare inferred RNA trajectories across all pipeline stages (UMAP).

plot_results_prot(p[, stim, prior, project_on_full])

Compare protein trajectories and simulations (UMAP colored by time).

Module Contents

CardamomOT.tools.plot_results_sim.plot_results_rna_mixture(split, p, project_on_full=False, normtransform=False, logtransform=True)

Compare observed data to the NB mixture fit (UMAP by time and cell type).

Parameters:

  • split (str) – Data split to load ("full" or "train").

  • p (str) – Path to the project directory (trailing slash included).

  • project_on_full (bool) – If True, fit UMAP on data and project mixture; otherwise fit jointly.

  • normtransform (bool) – Apply total-count normalisation before UMAP.

  • logtransform (bool) – Apply log1p transformation before UMAP.

CardamomOT.tools.plot_results_sim.plot_results_rna_clean(p, stim=1.0, prior=1.0, project_on_full=False, normtransform=False, logtransform=True)

Compare inferred RNA trajectories across all pipeline stages (UMAP).

Loads reference (NB mixture), network modes, RNA trajectories, and simulated data, then plots time and cell-type UMAPs for all four.

Parameters:

  • split (str) – Data split ("full" or "train").

  • p (str) – Path to the project directory (trailing slash included).

  • stim (float) – Stimulus-edge penalisation value used during inference.

  • prior (float) – Prior-network weighting value used during inference.

  • project_on_full (bool) – If True, fit UMAP on the NB mixture and project others.

  • normtransform (bool) – Apply total-count normalisation before UMAP.

  • logtransform (bool) – Apply log1p transformation before UMAP.

CardamomOT.tools.plot_results_sim.plot_results_prot(p, stim=1.0, prior=1.0, project_on_full=True)

Compare protein trajectories and simulations (UMAP colored by time).

Parameters:

  • p (str) – Path to the project directory (trailing slash included).

  • stim (float) – Stimulus-edge penalisation value used during inference.

  • prior (float) – Prior-network weighting value used during inference.

  • project_on_full (bool) – If True, fit UMAP on trajectories and project simulations.