---
name: omero-screen-plots
description: >
  Add your description here. Use when writing Python code that uses the omero_screen_plots package.
compatibility: Requires Python >=3.12,<3.15.
---

# OMERO-Screen Plots

Add your description here

## Installation

```bash
pip install omero-screen-plots
```

## API overview

### Cell cycle

Phase distributions and stacked composition plots.

- `cellcycle_plot`: Plot cell cycle phases in a 2x2 subplot grid with statistical analysis
- `cellcycle_stacked`: Create a stacked barplot for cell cycle phase proportions with flexible display modes
- `combplot_cellcycle`: Create a combined plot with histograms, scatter plots, and cell cycle barplot

### Counts and features

Cell counts, per-feature comparisons and normalisation.

- `count_plot`: Plot normalized or absolute counts with optional grouping
- `feature_plot`: Plot a unified feature plot with box/violin plots and optional scatter points
- `feature_norm_plot`: Create a normalized feature plot with threshold-based stacked bars
- `combplot_feature`: Create a combined plot with histograms and scatter plots for feature analysis
- `PlotType`: Enumeration for plot types: normalised and absolute

### Distributions

Histograms and scatter plots of single-cell measurements.

- `histogram_plot`: Create histogram plot(s) for single or multiple conditions
- `scatter_plot`: Create a scatter plot with flexible configuration

### Classification and QC

Classifier output and per-well quality control.

- `classification_plot`: Create a classification plot with flexible display options
- `well_qc_plot`: Build a compact per-well QC figure (histogram + scatter + cell-cycle bar)

### Utilities

- `save_fig`: Save a matplotlib figure to a file

## Resources

- [Full documentation](https://hocheggerlab.github.io/omero-screen/plots/)
- [llms.txt](llms.txt) — Indexed API reference for LLMs
- [llms-full.txt](llms-full.txt) — Comprehensive documentation for LLMs