mtopic.pl.zscores

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mtopic.pl.zscores#

mtopic.pl.zscores(mdata, mod, x, zscores='zscores', cmap=None, marker='.', s=10, fontsize=10, figsize=None, transparent=False, save=None)#

Visualize the spatial or embedding-based distribution of z-scores for topics in a specified modality.

This function generates scatter plots showing the distribution of z-scores for each topic in a specified modality of a MuData object. Z-scores are used to highlight spatial or embedding-based patterns of feature expression across samples, revealing significant variations relative to the global mean.

Parameters:

  • mdata (muon.MuData) – A MuData object containing multimodal single-cell data with z-scores stored in the obsm attribute.

  • mod (str) – The modality to visualize z-scores for (e.g., ‘rna’, ‘protein’).

  • x (str) – The key in obsm of mdata representing the spatial coordinates or embeddings to use for plotting (e.g., ‘coords’, ‘umap’).

  • zscores (str, optional) – The key in obsm of the specified modality representing the z-scores to plot. Default is ‘zscores’.

  • cmap (matplotlib.colors.Colormap or None, optional) – The colormap to use for visualizing z-scores. If None, a custom colormap is applied. Default is None.

  • marker (str, optional) – Marker style for scatter plots. Default is ‘.’.

  • s (int, optional) – Marker size for scatter plots. Default is 10.

  • fontsize (int, optional) – Font size for plot titles and colorbar ticks. Default is 10.

  • figsize (tuple, optional) – Tuple specifying the figure size (width, height) in inches. If None, the size is automatically determined based on the number of topics. Default is None.

  • transparent (bool, optional) – Whether to make the figure background transparent. Useful for overlays in presentations. Default is False.

  • save (str, optional) – Path to save the figure. If None, the figure is displayed but not saved. Default is None.

Returns:

None

Example:
import mtopic

# Load MuData object
mdata = mtopic.read.h5mu("path/to/file.h5mu")

# Visualize z-scores for topics in the 'rna' modality using spatial coordinates
mtopic.pl.zscores(
    mdata,
    mod='rna',
    x='coords',
    zscores='zscores',
    cmap='coolwarm',
    marker='o',
    s=15
)

# Save the figure to a file
mtopic.pl.zscores(
    mdata,
    mod='rna',
    x='umap',
    save='zscores_distribution.pdf'
)
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