`_column_plots`

Horizontal bar and log2 fold-change dotplot figure builders from _plotting/_column_plots.py.

These functions are the package’s main helpers for per-feature summary columns and composite bar-plus-dotplot layouts.

Public entry points

barh_column
l2fc_dotplot_single
l2fc_dotplot_column
barh_l2fc_dotplot_column
barh_dotplot_dotplot_column
barh_dotplot_dotplot_dotplot_column
barh_4X_dotplot_column

Shared data model

Most functions support one of these input paths:

adata, optionally with layer
explicit x_df, obs_df, and var_df

Shared expectations:

feature_list is required for every feature-oriented plot.
Bar panels read expression values from adata.X, adata.layers[layer], or x_df.
Dotplot panels read per-feature statistics from adata.var or var_df.
Grouping for bar plots comes from comparison_col in adata.obs or obs_df.

`barh_column`

Use barh_column(...) for a single column of horizontal grouped bar plots, with optional stripplot overlays.

Full signature

def barh_column(
        adata: anndata.AnnData | None = None,
        use_adata_raw: bool = False,
        layer: str | None =None,
        x_df: pd.DataFrame | None = None,
        var_df: pd.DataFrame | None = None,
        obs_df: pd.DataFrame | None = None,
        feature_list=None,
        feature_label_vars_col: str | None = None,# if None then index is used
        include_stripplot: bool = True,
        feature_label_char_limit: int | None= 25,
        feature_label_x: float = -0.02,
        figsize: tuple[int, int] = (10, 30),
        fig_title: str | None = None,
        fig_title_y: float | None = .99,
        fig_title_fontsize: int | None = 30,
        feature_label_fontsize: int | None= 24,
        tick_label_fontsize: int | None= 20,
        legend_fontsize: int | None= 24,
        tight_layout_rect_arg=[0, .05, 1, .99],
        comparison_col: str | None = 'Treatment',
        barh_remove_yticklabels: bool = True,
        comparison_order: list[str] | None = None,
        barh_subplot_xlabel: str | None = 'Expression (TPM)',
        barh_sharex: bool = False,
        barh_set_xaxis_lims: tuple[int, int]| None = None,
        barh_legend: bool = True,
        barh_legend_bbox_to_anchor: tuple[float, float] | None = (0.5, -.05),
        savefig: bool = False,
        file_name: str = 'test_plot.png'):

fig, axes = adtl.barh_column(
    adata=adata,
    layer="pgml",
    feature_list=["IL6", "TNF", "CXCL10"],
    comparison_col="Treatment",
    include_stripplot=True,
    savefig=True,
    file_name="results/barh_column.png",
)

Important behavior:

feature_list is required.
use_adata_raw=True switches to adata.raw.to_adata().
Sparse matrices are densified before building the plotting DataFrame.
comparison_order fixes category order when provided.
feature_label_vars_col is used for display labels when available; otherwise the feature index is used.
The function returns (fig, axes).

`l2fc_dotplot_single`

Use l2fc_dotplot_single(...) for one dotplot axis summarizing log2 fold change and p-value significance for a list of features.

Full signature

def l2fc_dotplot_single(
    adata: anndata.AnnData | None = None,
    var_df: pd.DataFrame | None = None,
    feature_list: list[str] | None = None,
    feature_label_vars_col: str | None = None,
    feature_label_char_limit: int | None = 25,
    figsize: tuple[int, int] = (8, 10),
    fig_title: str | None = None,
    fig_title_y: float = 1.02,
    feature_label_fontsize: int | None = 14,
    tick_label_fontsize: int | None = 12,
    legend_fontsize: int | None = 14,
    dotplot_pval_vars_col_label: str = 'pvalue',
    dotplot_l2fc_vars_col_label: str = 'log2FoldChange',
    dotplot_subplot_xlabel: str = 'log2fc ((target)/(ref))',
    pval_label: str = 'p-value',
    pvalue_cutoff_ring: float = 0.1,
    sizes: tuple[int, int] = (20, 2000),
    dotplot_set_xaxis_lims: tuple[int, int] | None = None,
    dotplot_legend: bool = True,
    dotplot_legend_bins: int | None = 4,
    dotplot_legend_bbox_to_anchor: tuple[float, float] = (0.5, -0.05),
    dotplot_annotate: bool = False,
    dotplot_annotate_fontsize: int | None = None,
):

fig, ax = adtl.l2fc_dotplot_single(
    adata=adata,
    feature_list=["IL6", "TNF", "CXCL10"],
    dotplot_pval_vars_col_label="pvalue",
    dotplot_l2fc_vars_col_label="log2FoldChange",
)

Important behavior:

Requires adata or var_df.
Requires both the p-value column and the log2 fold-change column in var_df.
Points below the threshold are greyed out.
A red ring marks the pvalue_cutoff_ring threshold in -log10(p) space.
The return value is (fig, ax).

`l2fc_dotplot_column`

Use l2fc_dotplot_column(...) for a vertically stacked column of one-feature-per-row dotplots.

Full signature

def l2fc_dotplot_column(
        # shared parameters
        adata: anndata.AnnData | None = None,
        var_df: pd.DataFrame | None = None,
        feature_list: list[str] | None = None,  # index of adata.var / var_df
        feature_label_vars_col: str | None = None,  # if None then index is used
        feature_label_char_limit: int | None = 25,
        feature_label_x: float = -0.02,
        figsize: tuple[int, int] | None = (8, 12),
        fig_title: str | None = None,
        fig_title_y: float = 1.03,
        subfig_title_fontsize: int | None = 24,
        feature_label_fontsize: int | None = 24,
        tick_label_fontsize: int | None = 20,
        legend_fontsize: int | None = 24,
        tight_layout_rect_arg: list[float] | None = [0, 0, 1, 1],
        savefig: bool = False,
        file_name: str = 'l2fc_dotplot.png',
        # dotplot specific parameters (mirrors barh_l2fc_dotplot_column)
        dotplot_figure_plot_title: str | None = 'log2fc',
        dotplot_pval_vars_col_label: str | None = 'pvalue',
        dotplot_l2fc_vars_col_label: str | None = 'log2FoldChange',
        dotplot_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        pval_label: str = 'p-value',
        pvalue_cutoff_ring: float = 0.1,
        sizes: tuple[int, int] | None = (20, 2000),
        dotplot_sharex: bool = False,
        dotplot_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot_legend: bool = True,
        dotplot_legend_bins: int | None = 4,
        dotplot_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.005),
        # Optional annotation on the dotplot with l2fc and p-value
        dotplot_annotate: bool = False,
        dotplot_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot_annotate_fontsize: int | None = None,
    ):

fig, axes = adtl.l2fc_dotplot_column(
    adata=adata,
    feature_list=feature_list,
    dotplot_pval_vars_col_label="paired_pvalue",
    dotplot_l2fc_vars_col_label="log2FoldChange",
    dotplot_sharex=True,
)

Important behavior:

Accepts adata or var_df.
Returns (fig, ax) for a single feature and (fig, axes) for multiple features.
Optional annotation text uses the current feature’s log2 fold change and p-value.

`barh_l2fc_dotplot_column`

This is the main composite plotting helper used in the example workflow.

Full signature

def barh_l2fc_dotplot_column(
        # shared parameters
        adata: anndata.AnnData | None = None,
        layer: str | None = None,
        x_df: pd.DataFrame | None = None,
        var_df: pd.DataFrame | None = None,
        obs_df: pd.DataFrame | None = None,
        feature_list: list[str] | None = None, # index of adata
        feature_label_vars_col: str | None = None, # if None than adata index used to label
        feature_label_char_limit: int | None = 40,
        feature_label_x: float = -0.02,
        figsize: tuple[int, int]| None = (10, 15),
        fig_title: str | None = None,
        fig_title_y: float = 1.03,
        subfig_title_y: float = 99,
        fig_title_fontsize: int | None = 30,
        subfig_title_fontsize: int | None = 24,
        feature_label_fontsize: int | None= 24,
        tick_label_fontsize: int | None= 20,
        legend_fontsize: int | None= 24,
        row_hspace: float | None = None,
        col_wspace: float | None = 0.07,
        bar2dotplot_width_ratios: list[float] | None = [1.5, 1.],
        tight_layout_rect_arg: list[float] | None = [0, 0, 1, 1],
        use_tight_layout: bool = True,
        savefig: bool = False,
        file_name: str = 'test_plot.png',
        # barh specific parameters
        comparison_col: str | None = 'Treatment',
        comparison_order: list[str] | None = None,
        hue_palette_color_list: list[str] | None = None,
        barh_remove_yticklabels: bool = True,
        barh_figure_plot_title: str | None = f'Expression (TPM)',
        barh_subplot_xlabel: str | None = 'Expression (TPM)',
        barh_sharex: bool = False,
        barh_set_xaxis_lims: tuple[int, int]| None = None,
        barh_legend: bool = True,
        barh_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),

        # dotplot specific parameters
        dotplot_figure_plot_title: str | None = 'log2fc',
        dotplot_pval_vars_col_label: str | None = 'pvalue',
        dotplot_l2fc_vars_col_label: str | None ='log2FoldChange',
        dotplot_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        pval_label: str = 'p-value',
        l2fc_label: str = 'log2FoldChange',
        pvalue_cutoff_ring: float = 0.1,
        sizes: tuple[int, int] | None = (20, 2000),
        dotplot_sharex: bool = False,
        dotplot_set_xaxis_lims: tuple[int, int]| None = None,
        dotplot_legend: bool = True,
        dotplot_legend_bins: int | None = 4,
        dotplot_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        # Optional annotation on the dotplot with l2fc and p-value
        dotplot_annotate: bool = False,
        dotplot_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot_annotate_fontsize: int | None = None,
        #
        ):

fig, subfigs = adtl.barh_l2fc_dotplot_column(
    adata=adata,
    layer="pgml",
    feature_list=feature_list,
    comparison_col="Treatment",
    dotplot_pval_vars_col_label="FDR",
    dotplot_l2fc_vars_col_label="log2FoldChange",
    savefig=True,
    file_name="results/barh_l2fc_dotplot.png",
)

Layout

left subfigure: grouped horizontal bars with optional stripplot overlay
right subfigure: one-feature-per-row log2 fold-change dotplots

Important behavior

Returns (fig, subfigs).
Supports either adata or explicit x_df plus obs_df plus var_df.
hue_palette_color_list overrides the category colors for the bar panel.
Dotplots derive marker color and size from -log10(p) and draw a red ring at the cutoff.
Legends for the bar and dot panels are controlled separately.

This is the function called by example_PMID_33969320/scripts/make_diff_datapoint_plots.py.

Advanced composite variants

The remaining functions extend the same pattern by adding more dotplot columns:

barh_dotplot_dotplot_column: bar column plus two dotplot columns
barh_dotplot_dotplot_dotplot_column: bar column plus three dotplot columns
barh_4X_dotplot_column: bar column plus four dotplot columns

Full signatures

def barh_dotplot_dotplot_column(
        # shared parameters
        adata: anndata.AnnData | None = None,
        layer: str | None = None,
        x_df: pd.DataFrame | None = None,
        var_df: pd.DataFrame | None = None,
        obs_df: pd.DataFrame | None = None,
        feature_list: list[str] | None = None,
        feature_label_vars_col: str | None = None,
        feature_label_char_limit: int | None = 40,
        feature_label_x: float = -0.02,
        figsize: tuple[int, int] | None = (14, 15),
        fig_title: str | None = None,
        fig_title_y: float = 1.03,
        subfig_title_y: float = 0.99,
        fig_title_fontsize: int | None = 30,
        subfig_title_fontsize: int | None = 24,
        feature_label_fontsize: int | None = 24,
        tick_label_fontsize: int | None = 20,
        legend_fontsize: int | None = 24,
        row_hspace: float | None = None,
        col_wspace: float | None = 0.07,
        bar_dotplot_width_ratios: list[float] | None = [1.5, 1.0, 1.0],
        tight_layout_rect_arg: list[float] | None = [0, 0, 1, 1], # [left, bottom, right, top]
        use_tight_layout: bool = True,
        savefig: bool = False,
        file_name: str = 'barh_dotplot_dotplot.png',
        # barh specific parameters
        comparison_col: str | None = 'Treatment',
        comparison_order: list[str] | None = None,
        hue_palette_color_list: list[str] | None = None,
        barh_remove_yticklabels: bool = True,
        barh_figure_plot_title: str | None = 'Expression (TPM)',
        barh_subplot_xlabel: str | None = 'Expression (TPM)',
        barh_sharex: bool = False,
        barh_set_xaxis_lims: tuple[int, int] | None = None,
        barh_legend: bool = True,
        barh_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        # dotplot1 parameters (match barh_l2fc_dotplot_column)
        dotplot_figure_plot_title: str | None = 'log2fc',
        dotplot_pval_vars_col_label: str | None = 'pvalue',
        dotplot_l2fc_vars_col_label: str | None = 'log2FoldChange',
        dotplot_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        pval_label: str = 'p-value',
        pvalue_cutoff_ring: float = 0.1,
        sizes: tuple[int, int] | None = (20, 2000),
        dotplot_sharex: bool = False,
        dotplot_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot_legend: bool = True,
        dotplot_legend_bins: int | None = 4,
        dotplot_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        dotplot_annotate: bool = False,
        dotplot_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot_annotate_fontsize: int | None = None,
        # dotplot2 parameters (alt)
        dotplot2_figure_plot_title: str | None = 'log2fc (2)',
        dotplot2_pval_vars_col_label: str | None = 'pvalue_alt',
        dotplot2_l2fc_vars_col_label: str | None = 'log2FoldChange_alt',
        dotplot2_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        dotplot2_pval_label: str = 'p-value',
        dotplot2_pvalue_cutoff_ring: float = 0.1,
        dotplot2_sizes: tuple[int, int] | None = (20, 2000),
        dotplot2_sharex: bool = False,
        dotplot2_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot2_legend: bool = True,
        dotplot2_legend_bins: int | None = 4,
        dotplot2_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        dotplot2_annotate: bool = False,
        dotplot2_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot2_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot2_annotate_fontsize: int | None = None,
        ):

def barh_dotplot_dotplot_dotplot_column(
        adata: anndata.AnnData | None = None,
        layer: str | None = None,
        x_df: pd.DataFrame | None = None,
        var_df: pd.DataFrame | None = None,
        obs_df: pd.DataFrame | None = None,
        feature_list: list[str] | None = None,
        feature_label_vars_col: str | None = None,
        feature_label_char_limit: int | None = 40,
        feature_label_x: float = -0.02,
        figsize: tuple[int, int] | None = (20, 25),
        fig_title: str | None = None,
        fig_title_y: float = 1.0,
        subfig_title_y: float = 0.94,
        fig_title_fontsize: int | None = 30,
        subfig_title_fontsize: int | None = 24,
        feature_label_fontsize: int | None = 24,
        tick_label_fontsize: int | None = 16,
        legend_fontsize: int | None = 20,
        row_hspace: float | None = None,
        col_wspace: float | None = 0.07,
        bar_dotplot_width_ratios: list[float] | None = [1.5, 1.0, 1.0, 1.0],
        tight_layout_rect_arg: list[float] | None = [0, 0, 1, 1],
        use_tight_layout: bool = True,
        savefig: bool = False,
        file_name: str = 'barh_dotplot_dotplot_dotplot.png',
        # barh
        comparison_col: str | None = 'Treatment',
        comparison_order: list[str] | None = None,
        hue_palette_color_list: list[str] | None = None,
        barh_remove_yticklabels: bool = True,
        barh_figure_plot_title: str | None = 'Expression',
        barh_subplot_xlabel: str | None = 'Expression',
        barh_sharex: bool = False,
        barh_set_xaxis_lims: tuple[int, int] | None = None,
        barh_legend: bool = True,
        barh_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        # dotplot1
        dotplot_figure_plot_title: str | None = 'log2fc',
        dotplot_pval_vars_col_label: str | None = 'pvalue',
        dotplot_l2fc_vars_col_label: str | None = 'log2FoldChange',
        dotplot_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        pval_label: str = 'p-value',
        pvalue_cutoff_ring: float = 0.1,
        sizes: tuple[int, int] | None = (20, 2000),
        dotplot_sharex: bool = False,
        dotplot_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot_legend: bool = True,
        dotplot_legend_bins: int | None = 4,
        dotplot_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        dotplot_annotate: bool = False,
        dotplot_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot_annotate_fontsize: int | None = None,
        # dotplot2
        dotplot2_figure_plot_title: str | None = 'log2fc (2)',
        dotplot2_pval_vars_col_label: str | None = 'pvalue_alt',
        dotplot2_l2fc_vars_col_label: str | None = 'log2FoldChange_alt',
        dotplot2_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        dotplot2_pval_label: str = 'p-value',
        dotplot2_pvalue_cutoff_ring: float = 0.1,
        dotplot2_sizes: tuple[int, int] | None = (20, 2000),
        dotplot2_sharex: bool = False,
        dotplot2_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot2_legend: bool = True,
        dotplot2_legend_bins: int | None = 4,
        dotplot2_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        dotplot2_annotate: bool = False,
        dotplot2_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot2_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot2_annotate_fontsize: int | None = None,
        # dotplot3
        dotplot3_figure_plot_title: str | None = 'log2fc (3)',
        dotplot3_pval_vars_col_label: str | None = 'pvalue_alt2',
        dotplot3_l2fc_vars_col_label: str | None = 'log2FoldChange_alt2',
        dotplot3_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        dotplot3_pval_label: str = 'p-value',
        dotplot3_pvalue_cutoff_ring: float = 0.1,
        dotplot3_sizes: tuple[int, int] | None = (20, 2000),
        dotplot3_sharex: bool = False,
        dotplot3_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot3_legend: bool = True,
        dotplot3_legend_bins: int | None = 4,
        dotplot3_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        dotplot3_annotate: bool = False,
        dotplot3_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot3_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot3_annotate_fontsize: int | None = None,
    ):

def barh_4X_dotplot_column(
        adata: anndata.AnnData | None = None,
        layer: str | None = None,
        x_df: pd.DataFrame | None = None,
        var_df: pd.DataFrame | None = None,
        obs_df: pd.DataFrame | None = None,
        feature_list: list[str] | None = None,
        feature_label_vars_col: str | None = None,
        feature_label_char_limit: int | None = 40,
        feature_label_x: float = -0.02,
        figsize: tuple[int, int] | None = (22, 25),
        fig_title: str | None = None,
        fig_title_y: float = 1.0,
        subfig_title_y: float = 0.94,
        fig_title_fontsize: int | None = 30,
        subfig_title_fontsize: int | None = 24,
        feature_label_fontsize: int | None = 24,
        tick_label_fontsize: int | None = 16,
        legend_fontsize: int | None = 20,
        row_hspace: float | None = None,
        col_wspace: float | None = 0.07,
        bar_dotplot_width_ratios: list[float] | None = [1.5, 1.0, 1.0, 1.0, 1.0],
        tight_layout_rect_arg: list[float] | None = [0, 0, 1, 1],
        use_tight_layout: bool = True,
        savefig: bool = False,
        file_name: str = 'barh_4X_dotplot.png',
        # barh
        comparison_col: str | None = 'Treatment',
        comparison_order: list[str] | None = None,
        hue_palette_color_list: list[str] | None = None,
        barh_remove_yticklabels: bool = True,
        barh_figure_plot_title: str | None = 'Expression',
        barh_subplot_xlabel: str | None = 'Expression',
        barh_sharex: bool = False,
        barh_set_xaxis_lims: tuple[int, int] | None = None,
        barh_legend: bool = True,
        barh_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        # dotplot1
        dotplot_figure_plot_title: str | None = 'log2fc',
        dotplot_pval_vars_col_label: str | None = 'pvalue',
        dotplot_l2fc_vars_col_label: str | None = 'log2FoldChange',
        dotplot_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        pval_label: str = 'p-value',
        pvalue_cutoff_ring: float = 0.1,
        sizes: tuple[int, int] | None = (20, 2000),
        dotplot_sharex: bool = False,
        dotplot_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot_legend: bool = True,
        dotplot_legend_bins: int | None = 4,
        dotplot_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        dotplot_annotate: bool = False,
        dotplot_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot_annotate_fontsize: int | None = None,
        # dotplot2
        dotplot2_figure_plot_title: str | None = 'log2fc (2)',
        dotplot2_pval_vars_col_label: str | None = 'pvalue_alt',
        dotplot2_l2fc_vars_col_label: str | None = 'log2FoldChange_alt',
        dotplot2_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        dotplot2_pval_label: str = 'p-value',
        dotplot2_pvalue_cutoff_ring: float = 0.1,
        dotplot2_sizes: tuple[int, int] | None = (20, 2000),
        dotplot2_sharex: bool = False,
        dotplot2_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot2_legend: bool = True,
        dotplot2_legend_bins: int | None = 4,
        dotplot2_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        dotplot2_annotate: bool = False,
        dotplot2_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot2_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot2_annotate_fontsize: int | None = None,
        # dotplot3
        dotplot3_figure_plot_title: str | None = 'log2fc (3)',
        dotplot3_pval_vars_col_label: str | None = 'pvalue_alt2',
        dotplot3_l2fc_vars_col_label: str | None = 'log2FoldChange_alt2',
        dotplot3_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        dotplot3_pval_label: str = 'p-value',
        dotplot3_pvalue_cutoff_ring: float = 0.1,
        dotplot3_sizes: tuple[int, int] | None = (20, 2000),
        dotplot3_sharex: bool = False,
        dotplot3_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot3_legend: bool = True,
        dotplot3_legend_bins: int | None = 4,
        dotplot3_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        dotplot3_annotate: bool = False,
        dotplot3_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot3_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot3_annotate_fontsize: int | None = None,
        # dotplot4
        dotplot4_figure_plot_title: str | None = 'log2fc (4)',
        dotplot4_pval_vars_col_label: str | None = 'pvalue_alt3',
        dotplot4_l2fc_vars_col_label: str | None = 'log2FoldChange_alt3',
        dotplot4_subplot_xlabel: str | None = 'log2fc ((target)/(ref))',
        dotplot4_pval_label: str = 'p-value',
        dotplot4_pvalue_cutoff_ring: float = 0.1,
        dotplot4_sizes: tuple[int, int] | None = (20, 2000),
        dotplot4_sharex: bool = False,
        dotplot4_set_xaxis_lims: tuple[int, int] | None = None,
        dotplot4_legend: bool = True,
        dotplot4_legend_bins: int | None = 4,
        dotplot4_legend_bbox_to_anchor: tuple[int, int] | None = (0.5, -.05),
        dotplot4_annotate: bool = False,
        dotplot4_annotate_xy: tuple[float, float] | None = (0.8, 1.2),
        dotplot4_annotate_labels: tuple[str, str] | None = ('l2fc: ', 'p:'),
        dotplot4_annotate_fontsize: int | None = None,
        use_single_dotplot_colormap: bool = False,
    ):

Each added dotplot column gets its own parameter family:

dotplot2_*
dotplot3_*
dotplot4_* for barh_4X_dotplot_column

Important behavior:

These functions still return (fig, subfigs).
Every added dotplot panel requires its own *_pval_vars_col_label and *_l2fc_vars_col_label.
hue_palette_color_list must provide at least one color per comparison_col category when used.
These layouts are best treated as configuration-heavy report builders rather than small convenience wrappers.

Common caveats

Many functions call plt.show() internally.
savefig=True writes the figure with plt.savefig(...).
Missing required features raise early KeyError or ValueError.
There do not appear to be dedicated regression tests for this module; this page is based on current code and the example plotting scripts.

_column_plots

Public entry points

Shared data model

barh_column

Full signature

l2fc_dotplot_single

Full signature

l2fc_dotplot_column

Full signature

barh_l2fc_dotplot_column

Full signature

Layout

Important behavior

Advanced composite variants

Full signatures

Common caveats

`_column_plots`

`barh_column`

`l2fc_dotplot_single`

`l2fc_dotplot_column`

`barh_l2fc_dotplot_column`