mmcontext.pl.plotting.plot_query_scores_with_labels_umap

mmcontext.pl.plotting.plot_query_scores_with_labels_umap#

mmcontext.pl.plotting.plot_query_scores_with_labels_umap(adata, queries, labels, label_key, embedding_key='X_umap', emb_key='mmcontext_emb', save_plot=True, save_dir=None, nametag=None, figsize=(6, 6), dpi=300, point_size=5, frameon=False, legend_fontsize=10, font_weight='normal', font_style='normal', font_size=12, axis_label_size=12, axis_tick_size=10, save_format='png', umap_n_neighbors=15, umap_min_dist=0.1, umap_random_state=42, **kwargs)#

Plot UMAPs colored by query similarity scores with label highlighting.

This function creates UMAP plots where: 1. Points are colored by similarity scores for each query 2. Points corresponding to specific labels are highlighted with borders 3. Query strings are saved as titles in separate plots 4. Verification is performed to ensure labels match queries and exist in adata.obs

Parameters:

  • adata (anndata.AnnData) – AnnData object containing query_scores in .obs and embeddings in .obsm

  • queries (list[str]) – List of query strings to plot. Must match keys in adata.obs[“query_scores”]

  • labels (list[str]) – List of label names, one per query (same length as queries)

  • label_key (str) – Key in adata.obs containing the label information

  • embedding_key (str, optional) – Key in adata.obsm containing UMAP coordinates. If not present, UMAP will be computed. Defaults to “X_umap”

  • emb_key (str, optional) – Key in adata.obsm containing embeddings for UMAP computation. Defaults to “mmcontext_emb”

  • save_plot (bool, optional) – Whether to save plots. Defaults to True

  • save_dir (str, optional) – Directory to save plots. Defaults to None

  • nametag (str, optional) – Additional tag for saved files. Defaults to None

  • figsize (tuple, optional) – Figure size (width, height). Defaults to (6, 6)

  • dpi (int, optional) – DPI for saved plots. Defaults to 300

  • point_size (int, optional) – Size of scatter plot points. Defaults to 5

  • frameon (bool, optional) – Whether to show plot frame. Defaults to False

  • legend_fontsize (int, optional) – Font size for legends. Defaults to 10

  • font_weight (str, optional) – Font weight. Defaults to “normal”

  • font_style (str, optional) – Font style. Defaults to “normal”

  • font_size (int, optional) – General font size. Defaults to 12

  • axis_label_size (int, optional) – Axis label font size. Defaults to 12

  • axis_tick_size (int, optional) – Axis tick font size. Defaults to 10

  • save_format (str, optional) – Format for saved plots. Defaults to “png”

  • umap_n_neighbors (int, optional) – Number of neighbors for UMAP computation. Defaults to 15

  • umap_min_dist (float, optional) – Minimum distance for UMAP computation. Defaults to 0.1

  • umap_random_state (int, optional) – Random state for UMAP computation. Defaults to 42

  • **kwargs – Additional keyword arguments

Returns:

None Saves or displays UMAP plots

Raises:

ValueError – If validation checks fail

Examples

>>> plot_query_scores_with_labels_umap(
...     adata=adata,
...     queries=["T cell", "B cell"],
...     labels=["T_cell", "B_cell"],
...     label_key="cell_type",
...     save_dir="plots/query_analysis",
... )
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