Plots

Plotting Functions

immunopheno.plots.plot_UMAP(IPD: ImmunoPhenoData, normalized: bool = False, force_update: bool = False, random_state: int = 42, **kwargs)

Plots a UMAP for the non-normalized protein values or normalized protein values

Parameters:

  • IPD (ImmunoPhenoData Object) – object containing protein data, gene data, and cell types

  • normalized (bool) – option to plot normalized values

  • force_update (bool) – option to compute a new UMAP, replacing stored plots

  • random_state (int) – seed value for generating the UMAP

  • **kwargs – various arguments to UMAP class constructor, including default values: n_neighbors (int): 15 min_dist (float): 0.1 n_components (int): 2 metric (str): “euclidean”

Returns:

UMAP projection of non/normalized protein values with a corresponding legend of cell type (if available)

Return type:

go.Figure

immunopheno.plots.plot_filter_metrics(IPD: ImmunoPhenoData)

Plots a histogram of all D1/D2 distance ratios and entropies returned from run_stvea()

Parameters:

IPD (ImmunoPhenoData Object) – object must contain table containing distance ratios and entropies. These are stored in the object after calling run_stvea() from the ImmunoPhenoDB_Connect class.

Returns:

None. Renders two plotly histograms.

immunopheno.models.plot_ab_fit(IPD, ab: str, width: int | None = None)

Plots an antibody histogram and mixture model fits

Parameters:

  • IPD (ImmunoPhenoData Object) – Object containing all fits from mixture models

  • ab (str) – name of antibody to retrieve fits

  • width (int) – display width of all the graphs (optional)

Returns:

None. Renders a series of plots (1, 2, 3 component mixture models) for an antibody after fitting with a negative binomial or gaussian curve.

immunopheno.models.plot_all_fits(IPD, width: int | None = None)

Plots all antibody histograms and mixture model fits

Parameters:

  • IPD (ImmunoPhenoData Object) – Object containing all fits from mixture models

  • width (int) – display width of all the graphs (optional)

Returns:

None. Renders a series of plots with each type of mixture model for every antibody in the protein data