# Plotting

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

Plotting functions return Matplotlib axes and do not modify the object.

## Plates and quality control

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

    pl.plate
    pl.cell_counts
    pl.feature_distributions
    pl.nan_matrix
    pl.qc
    pl.plate_effects
    pl.image_qc
    pl.control_drift
    pl.outliers
```

## Features

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

    pl.feature_correlation
    pl.feature_groups
```

## Replicates and reproducibility

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

    pl.map
    pl.replicate_correlation
    pl.similarity
    pl.setting_agreement
    pl.transport
    pl.replicate_saturation
```

## Batch correction

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

    pl.batch_variance
    pl.metrics
```

## Hits and effect sizes

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

    pl.hits
    pl.effect_sizes
    pl.feature_volcano
    pl.feature_signature
    pl.cytotoxicity
```

## Dose response

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

    pl.dose_response
    pl.dose_direction
```

## Mechanism of action

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

    pl.moa_confusion
    pl.moa_enrichment
    pl.distance_heatmap
```

## Feature sets

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

    pl.sets_heatmap
```

## Clusters and gene sets

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

    pl.dendrogram
    pl.pathway_coherence
```

## Single cells

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

    pl.cluster_composition
    pl.cell_cycle
    pl.density
    pl.subpopulation_hits
```