"""
Visualization module for spatial transcriptomics.
Refactored architecture with 11 unified plot_types:
- feature: Spatial/UMAP feature visualization (basis='spatial'|'umap')
- expression: Aggregated expression (subtype='heatmap'|'violin'|'dotplot'|'correlation')
- deconvolution: Cell type proportions (subtype='spatial_multi'|'pie'|'dominant'|'diversity'|'umap'|'imputation')
- communication: Cell-cell communication (subtype='dotplot'|'tileplot'|'circle_plot')
- interaction: Spatial ligand-receptor pairs
- trajectory: Pseudotime and fate analysis (subtype='pseudotime'|'circular'|'fate_map'|'gene_trends'|'fate_heatmap'|'palantir')
- velocity: RNA velocity visualization (subtype='stream'|'phase'|'proportions'|'heatmap'|'paga')
- statistics: Spatial statistics (subtype='neighborhood'|'co_occurrence'|'ripley'|'moran'|'centrality'|'getis_ord')
- enrichment: Pathway enrichment (subtype='barplot'|'dotplot')
- cnv: Copy number variation (subtype='heatmap'|'spatial')
- integration: Batch integration quality (subtype='batch'|'cluster'|'highlight')
Usage:
from chatspatial.tools.visualization import visualize_data, PLOT_HANDLERS
"""
from .cell_comm import create_cell_communication_visualization
from .cnv import create_cnv_visualization
# Core utilities and data classes
from .core import (
FIGURE_DEFAULTS,
CellCommunicationData,
DeconvolutionData,
add_colorbar,
create_figure,
create_figure_from_params,
get_categorical_cmap,
get_category_colors,
get_colormap,
get_diverging_colormap,
get_validated_features,
plot_spatial_feature,
resolve_figure_size,
setup_multi_panel_figure,
validate_and_prepare_feature,
)
from .deconvolution import create_deconvolution_visualization
from .enrichment import create_pathway_enrichment_visualization
from .expression import create_expression_visualization
# Unified visualization handlers
from .feature import create_feature_visualization
from .integration import create_batch_integration_visualization
# Main entry point and handler registry
from .main import PLOT_HANDLERS, visualize_data
from .multi_gene import create_spatial_interaction_visualization
from .spatial_stats import create_spatial_statistics_visualization
from .trajectory import create_trajectory_visualization
from .velocity import create_rna_velocity_visualization
__all__ = [
# Core utilities
"FIGURE_DEFAULTS",
"create_figure",
"create_figure_from_params",
"resolve_figure_size",
"setup_multi_panel_figure",
"add_colorbar",
"get_colormap",
"get_categorical_cmap",
"get_category_colors",
"get_diverging_colormap",
"plot_spatial_feature",
"get_validated_features",
"validate_and_prepare_feature",
# Data classes
"DeconvolutionData",
"CellCommunicationData",
# Main entry point
"visualize_data",
# Handler registry
"PLOT_HANDLERS",
# Unified visualization handlers
"create_feature_visualization",
"create_expression_visualization",
"create_deconvolution_visualization",
"create_cell_communication_visualization",
"create_spatial_interaction_visualization",
"create_trajectory_visualization",
"create_rna_velocity_visualization",
"create_spatial_statistics_visualization",
"create_pathway_enrichment_visualization",
"create_cnv_visualization",
"create_batch_integration_visualization",
]
