scvi.external.scviva.differential_expression.DifferentialExpressionResults

scvi.external.scviva.differential_expression.DifferentialExpressionResults#

class scvi.external.scviva.differential_expression.DifferentialExpressionResults(gpc, g1_g2, g1_n1, n1_g2, n1_n2=None, n1_index=None, n2_index=None)[source]#

Bases: object

Dataclass for storing the results of the differential expression analysis, including the GP classifier

Attributes table#

n1_index

n1_n2

n2_index

gpc

g1_g2

g1_n1

n1_g2

Methods table#

gpc_info()

Print the log marginal likelihood value and the kernel of the Gaussian Process Classifier

plot([X, y, filter, background_filter, ...])

Plot the results of the differential expression analysis.

Attributes#

DifferentialExpressionResults.n1_index: ndarray | None = None#
DifferentialExpressionResults.n1_n2: DataFrame | None = None#
DifferentialExpressionResults.n2_index: ndarray | None = None#
DifferentialExpressionResults.gpc: GaussianProcessClassifier#
DifferentialExpressionResults.g1_g2: DataFrame#
DifferentialExpressionResults.g1_n1: DataFrame#
DifferentialExpressionResults.n1_g2: DataFrame#

Methods#

DifferentialExpressionResults.gpc_info()[source]#

Print the log marginal likelihood value and the kernel of the Gaussian Process Classifier

DifferentialExpressionResults.plot(X=None, y=None, filter=None, background_filter=None, markersize=50, fontsize=10, chosen_colormap='seismic', path_to_save=None, show_plot=True, dpi=1000, margin=0.1, manual_limits=None, legend_loc='upper right')[source]#

Plot the results of the differential expression analysis.

Parameters:

  • X (DataFrame | None (default: None)) – Design matrix: log fold changes for group 1 vs group 2 and neighbors 1 vs group 2. If None, the design matrix from the classifier is used.

  • y (Series | None (default: None)) – Labels: FDR values for group 1 vs neighbors 1. If None, the labels from the classifier are used.

  • filter (Iterable | None (default: None)) – Genes to include in the plot.

  • background_filter (Iterable | None (default: None)) – Genes to include in the plot as background.

  • markersize (int (default: 50)) – Size of the markers.

  • fontsize (int (default: 10)) – Font size for the gene names.

  • chosen_colormap (str (default: 'seismic')) – Colormap to use for the decision boundary.

  • path_to_save (str | None (default: None)) – Path to save the plot.

  • show_plot (bool (default: True)) – Whether to show the plot. Default: True.

  • dpi (int (default: 1000)) – Resolution of the saved plot.

  • margin (float (default: 0.1)) – Margin to add to the plot limits.

  • manual_limits (tuple | None (default: None)) – Manual limits for the plot.

  • legend_loc (str (default: 'upper right')) – Location of the legend.

Return type:

None

Returns:

None