`visualize_multimodal_embedding`¶

Flexible scatter-plot visualization of the multi-omics sample embeddings. When called with show_default=True (the default), renders side-by-side plots of the single-key sample embedding X_DR_sample with every sample visible. When modality_col, color_col, and target_modality are all provided, highlights one modality and colors by an arbitrary .obs column. visualization_grouping_column fans out additional colored panels — one per column — on top of whatever base layout you requested.

The expression_key / proportion_key arguments survive for backward compatibility but now both default to the same single key, X_DR_sample (the unified sample embedding produced by compute_sample_embedding); the two-key X_DR_expression / X_DR_proportion layout no longer exists.

Import: from sampledisco.visualization.multi_omics_visualization import visualize_multimodal_embedding

Source: sampledisco/visualization/multi_omics_visualization.py:497

Signature¶

def visualize_multimodal_embedding(
    adata,
    modality_col=None,
    color_col=None,
    target_modality=None,
    expression_key="X_DR_sample",
    proportion_key="X_DR_sample",
    figsize=(20, 8),
    point_size=60,
    alpha=0.8,
    colormap="viridis",
    categorical_cmap="tab10",
    output_dir=None,
    show_sample_names=False,
    force_data_type=None,
    show_default=True,
    verbose=True,
    visualization_grouping_column=None,
)

Parameters¶

Name	Type	Default	Description
`adata`	AnnData	—	Sample-level AnnData with the sample embedding in `.obsm` or `.uns` (`X_DR_sample`).
`modality_col`	str, optional	`None`	`.obs` column marking modality (required for modality-specific plots).
`color_col`	str, optional	`None`	`.obs` column for point coloring (required when not using default plot).
`target_modality`	str, optional	`None`	Which modality to highlight in modality-specific plots.
`expression_key`	str	`"X_DR_sample"`	Key in `.obsm`/`.uns` for the "Expression" panel. Back-compat alias — now the single sample-embedding key.
`proportion_key`	str	`"X_DR_sample"`	Key in `.obsm`/`.uns` for the "Proportion" panel. Back-compat alias — now the same single key.
`figsize`	tuple	`(20, 8)`	Matplotlib figure size.
`point_size`	int	`60`	Scatter marker size.
`alpha`	float	`0.8`	Marker opacity.
`colormap`	str	`"viridis"`	Colormap for numerical `color_col` values.
`categorical_cmap`	str	`"tab10"`	Colormap for categorical `color_col` values.
`output_dir`	str, optional	`None`	File or directory. Each generated panel is saved under a descriptive filename.
`show_sample_names`	bool	`False`	Overlay sample IDs — best left off unless you have few samples.
`force_data_type`	`"numerical"` / `"categorical"` / `None`	`None`	Override the auto-detection for `color_col`.
`show_default`	bool	`True`	Always produce the default side-by-side view without requiring modality args.
`verbose`	bool	`True`	Print progress.
`visualization_grouping_column`	list, optional	`None`	Extra `.obs` columns; generates one colored panel per entry.

Returns¶

Tuple[matplotlib.figure.Figure, numpy.ndarray] — the figure and axes array when the plots are rendered, None when saved separately.

Output files¶

Under {output_dir}/:

all_samples_expression.png, all_samples_proportion.png — default panel pair (both drawn from the single X_DR_sample key).
all_samples_combined.png — default side-by-side combined panel.
all_samples_expression_by_{col}.png, all_samples_proportion_by_{col}.png — per grouping column.
all_samples_combined_by_{col}.png — combined side-by-side with shared colorbar.
{target_modality}_modality_split_by_{col}.png — modality-specific view when all of modality_col, color_col, target_modality are supplied.

Usage¶

from sampledisco.visualization.multi_omics_visualization import visualize_multimodal_embedding

visualize_multimodal_embedding(
    adata=pseudo_adata,
    modality_col="modality",
    target_modality="ATAC",
    color_col=None,
    expression_key="X_DR_sample",
    proportion_key="X_DR_sample",
    visualization_grouping_column=["sev.level"],
    figsize=(20, 8),
    point_size=60,
    alpha=0.8,
    colormap="viridis",
    output_dir="sampledisco_demo_output/multiomics/visualization",
    show_default=True,
)