# API

## Basic plots

```{eval-rst}
.. module:: troutpy.pl
.. currentmodule:: troutpy.pl

.. autosummary::
    :toctree: generated/basic_plots

    crosstab
    histogram
    pie
    coupled_scatter
    point_metric_comparison
    heatmap
    sorted_heatmap
    spatial_transcripts
```

## uRNA quantification

```{eval-rst}
.. autosummary::
    :toctree: generated/quantification

    gene_metric_heatmap
    logfoldratio_over_noise
    metric_scatter
    top_bottom_probes
    genes_over_noise
    intra_extra_density
    moranI_histogram
    diffusion_results
    spatial_inout_expression

```

## Source, target and communication

```{eval-rst}
.. autosummary::
    :toctree: generated/communication

    cell_type_contacts
    celltype_contact_matrix
    gene_communication
    global_distribution_from_source
    distributions_by_cluster
    gene_distribution_from_source
    source_score_by_celltype
    target_score_by_celltype
    spatial_transcripts_source
    urna_vs_source_score
    interactions_with_arrows
    spatial_interactions

```

## Factor analysis

```{eval-rst}
.. autosummary::
    :toctree: generated/factor_analysis

    factors_in_cells
    rank_factor_genes_loadings
    rank_factor_genes_loadings_matrixplot
    nmf_factors_exrna_cells_W
    nmf_gene_contributions
    paired_nmf_factors
    apply_exrnaH_to_cellular_to_create_cellularW

```

## Colormaps & palettes

```{eval-rst}
.. autosummary::
    :toctree: generated/colormaps

    get_colormap
    get_palette
```