# omero_screen_plots

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## Docs

### API Reference

#### Cell cycle
> Phase distributions and stacked composition plots.

- [cellcycle_plot](https://hocheggerlab.github.io/omero-screen/plots/reference/cellcycle_plot.html): Plot cell cycle phases in a 2x2 subplot grid with statistical analysis
- [cellcycle_stacked](https://hocheggerlab.github.io/omero-screen/plots/reference/cellcycle_stacked.html): Create a stacked barplot for cell cycle phase proportions with flexible display modes
- [combplot_cellcycle](https://hocheggerlab.github.io/omero-screen/plots/reference/combplot_cellcycle.html): Create a combined plot with histograms, scatter plots, and cell cycle barplot

#### Counts and features
> Cell counts, per-feature comparisons and normalisation.

- [count_plot](https://hocheggerlab.github.io/omero-screen/plots/reference/count_plot.html): Plot normalized or absolute counts with optional grouping
- [feature_plot](https://hocheggerlab.github.io/omero-screen/plots/reference/feature_plot.html): Plot a unified feature plot with box/violin plots and optional scatter points
- [feature_norm_plot](https://hocheggerlab.github.io/omero-screen/plots/reference/feature_norm_plot.html): Create a normalized feature plot with threshold-based stacked bars
- [combplot_feature](https://hocheggerlab.github.io/omero-screen/plots/reference/combplot_feature.html): Create a combined plot with histograms and scatter plots for feature analysis
- [PlotType](https://hocheggerlab.github.io/omero-screen/plots/reference/PlotType.html): Enumeration for plot types: normalised and absolute

#### Distributions
> Histograms and scatter plots of single-cell measurements.

- [histogram_plot](https://hocheggerlab.github.io/omero-screen/plots/reference/histogram_plot.html): Create histogram plot(s) for single or multiple conditions
- [scatter_plot](https://hocheggerlab.github.io/omero-screen/plots/reference/scatter_plot.html): Create a scatter plot with flexible configuration

#### Classification and QC
> Classifier output and per-well quality control.

- [classification_plot](https://hocheggerlab.github.io/omero-screen/plots/reference/classification_plot.html): Create a classification plot with flexible display options
- [well_qc_plot](https://hocheggerlab.github.io/omero-screen/plots/reference/well_qc_plot.html): Build a compact per-well QC figure (histogram + scatter + cell-cycle bar)

#### Utilities

- [save_fig](https://hocheggerlab.github.io/omero-screen/plots/reference/save_fig.html): Save a matplotlib figure to a file