Index

A

adata (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) angle_bins_deg (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

annotate_cells() (scomv.cell_pipeline.CellPolarPipeline method) (scomv.CellPolarPipeline method)

B

bin_size (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) bin_size_um (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute)

build_distance() (scomv.cell_pipeline.CellPolarPipeline method) (scomv.CellPolarPipeline method) build_polar_distributions_for_genes() (scomv.gene_pipeline.SCOMVPipeline method) (scomv.SCOMVPipeline method)

C

cell_df (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) cell_df_filtered (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) cell_polar_maps() (scomv.cell_pipeline.CellPolarPipeline method) (scomv.CellPolarPipeline method) cell_similarity_matrix() (scomv.cell_pipeline.CellPolarPipeline static method) (scomv.CellPolarPipeline static method) CellPolarPipeline (class in scomv) (class in scomv.cell_pipeline) cluster_col (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) components_ (scomv.Spatial_DEG property) (scomv.spatial_deg.Spatial_DEG property)

compute_moran_df() (scomv.gene_pipeline.SCOMVPipeline method) (scomv.SCOMVPipeline method) contour_bounds (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) coord_col (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) coords (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) counts_by_cluster (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) cumulative_variance_ratio_ (scomv.Spatial_DEG property) (scomv.spatial_deg.Spatial_DEG property)

D

dendrogram2newick() (in module scomv) dist_df (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

E

explained (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

explained_variance_ratio_ (scomv.Spatial_DEG property) (scomv.spatial_deg.Spatial_DEG property)

F

filtered_shortest (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) fit() (scomv.Spatial_DEG method) (scomv.spatial_deg.Spatial_DEG method)

fit_umap_on_loadings() (scomv.Spatial_DEG method) (scomv.spatial_deg.Spatial_DEG method)

G

gene_lens (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) gene_total_counts_int() (scomv.gene_pipeline.SCOMVPipeline static method) (scomv.SCOMVPipeline static method) get_loadings_df() (scomv.Spatial_DEG method) (scomv.spatial_deg.Spatial_DEG method)

get_top_genes_signed() (scomv.Spatial_DEG method) (scomv.spatial_deg.Spatial_DEG method) grid (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

H

heatmap() (scomv.cell_pipeline.CellPolarPipeline method) (scomv.CellPolarPipeline method)

I

inside_points (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

invert_y (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

L

last_roi (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

loadings_ (scomv.Spatial_DEG property) (scomv.spatial_deg.Spatial_DEG property)

M

make_inside_negative (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) max_gene_percentile (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) min_cells (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) min_gene_percentile (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) min_vector_df (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

minas_similarity_matrix() (scomv.gene_pipeline.SCOMVPipeline static method) (scomv.SCOMVPipeline static method) module scomv scomv.cell_pipeline scomv.gene_pipeline scomv.spatial_deg moran_df (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

O

outline_points (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

P

p_high (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) p_low (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) pcoa_res (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) plot_3d() (in module scomv) plot_explained_variance() (scomv.cell_pipeline.CellPolarPipeline method) (scomv.CellPolarPipeline method) plot_explained_variance_bar() (scomv.Spatial_DEG method) (scomv.spatial_deg.Spatial_DEG method)

plot_loading_violin() (scomv.Spatial_DEG method) (scomv.spatial_deg.Spatial_DEG method) plot_pcoa_plotly() (scomv.gene_pipeline.SCOMVPipeline static method) (scomv.SCOMVPipeline static method) plot_signed_top_contributions() (scomv.Spatial_DEG method) (scomv.spatial_deg.Spatial_DEG method) plot_signed_top_contributions_multi() (scomv.Spatial_DEG method) (scomv.spatial_deg.Spatial_DEG method) plot_umap_loadings_interactive() (scomv.Spatial_DEG method) (scomv.spatial_deg.Spatial_DEG method) polar_counts_list (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

R

radius_bins (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute) (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) region_col (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) require_moran_nonneg (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

run() (scomv.cell_pipeline.CellPolarPipeline method) (scomv.CellPolarPipeline method) (scomv.gene_pipeline.SCOMVPipeline method) (scomv.SCOMVPipeline method) run_pcoa() (scomv.cell_pipeline.CellPolarPipeline method) (scomv.CellPolarPipeline method) run_pcoa_from_distance_df() (scomv.gene_pipeline.SCOMVPipeline static method) (scomv.SCOMVPipeline static method)

S

scomv module scomv.cell_pipeline module scomv.gene_pipeline module scomv.spatial_deg module SCOMVPipeline (class in scomv) (class in scomv.gene_pipeline) selected_clusters (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute)

selected_genes (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) Spatial_DEG (class in scomv) (class in scomv.spatial_deg) subsample_fraction (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute) subset_by_roi() (scomv.gene_pipeline.SCOMVPipeline static method) (scomv.SCOMVPipeline static method) subset_grid (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

U

unlabeled_name (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute)

X

x_col (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute)

xy_list (scomv.gene_pipeline.SCOMVPipeline attribute) (scomv.SCOMVPipeline attribute)

Y

y_col (scomv.cell_pipeline.CellPolarPipeline attribute) (scomv.CellPolarPipeline attribute)