# Cell cycle plots

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The cell cycle plot provides comprehensive visualization of cell cycle phase distributions across experimental conditions in a multi-panel grid layout with statistical analysis and flexible phase terminology.

See the [API reference](../reference/index.md) for full signatures and parameter documentation.


# Examples


## Default Cell Cycle Analysis

Create a standard 2x3 grid showing all cell cycle phases with statistical analysis:

``` python
from omero_screen_plots import cellcycle_plot
import pandas as pd

df = pd.read_csv("data.csv")
fig, axes = cellcycle_plot(
    df=df,
    conditions=['control', 'cond01', 'cond02', 'cond03'],
    condition_col="condition",
    selector_col="cell_line",
    selector_val="MCF10A",
    title="Cell Cycle Analysis",
    save=True,
    file_format="svg"
)
```


<figure class="figure">
<p><img src="../assets/cellcycle_plot_default.svg" class="img-fluid figure-img" /></p>
<figcaption>Default Cell Cycle Analysis</figcaption>
</figure>


## DNA Content Visualization

Focus on DNA content measurements with 2x2 grid layout:

``` python
fig, axes = cellcycle_plot(
    df=df,
    conditions=['control', 'cond01', 'cond02', 'cond03'],
    condition_col="condition",
    selector_col="cell_line",
    selector_val="MCF10A",
    cc_phases=False,  # Use DNA content terminology (<2N, 2N, S, 4N, >4N)
    title="DNA Content Analysis"
)
```


<figure class="figure">
<p><img src="../assets/cellcycle_plot_DNA_content.svg" class="img-fluid figure-img" /></p>
<figcaption>DNA Content Visualization</figcaption>
</figure>


## Custom Phase Selection

Analyze specific cell cycle phases with custom terminology:

``` python
fig, axes = cellcycle_plot(
    df=df,
    conditions=['control', 'cond01', 'cond02', 'cond03'],
    condition_col="condition",
    selector_col="cell_line",
    selector_val="MCF10A",
    cc_phases=True,
    show_subG1=False,  # Exclude SubG1
    title="Major Cell Cycle Phases"
)
```


<figure class="figure">
<p><img src="../assets/cellcycle_plot_no_SubG1.svg" class="img-fluid figure-img" /></p>
<figcaption>Custom Phase Selection</figcaption>
</figure>


## Clean Layout with Custom Colors

Create publication-ready figures with custom styling:

``` python
from omero_screen_plots.colors import COLOR

custom_colors = [COLOR.LIGHT_BLUE.value, COLOR.BLUE.value,
                 COLOR.GREY.value, COLOR.DARK_GREY.value]

fig, axes = cellcycle_plot(
    df=df,
    conditions=['control', 'cond01', 'cond02', 'cond03'],
    condition_col="condition",
    selector_col="cell_line",
    selector_val="MCF10A",
    show_subG1=True,
    colors=custom_colors,
    show_repeat_points=False,
    title="Custom Styled Cell Cycle"
)
```


<figure class="figure">
<p><img src="../assets/cellcycle_plot_custom_colors.svg" class="img-fluid figure-img" /></p>
<figcaption>Clean Layout with Custom Colors</figcaption>
</figure>