dotools_py.pl.umap

dotools_py.pl.umap(adata, color, split_by=None, catgs_order=None, figsize=(6, 5), ax=None, ncols=4, title=None, title_fontproperties=None, share_legend=False, vmax=None, spacing=(0.3, 0.2), path=None, filename='Umap.svg', show=True, labels=None, labels_fontproperties=None, labels_repel=None, **kwargs)

Scatter plot in UMAP basis.

This function builds on sc.pl.umap() and add extra functionalities like.

Parameters:

adata AnnData

Annotated data matrix.

color str | list

Keys for annotations of observations/cells or variables/genes.

split_by str | None (default: None)

Categorical column in adata.obs to split by.

catgs_order list (default: None)

Order of the categories when splitting by a categorical column.

figsize tuple[float, float] (default: (6, 5))

Figure size, the format is (width, height).

ax Axes (default: None)

Matplotlib axes to use for plotting. If not set, a new figure will be generated.

ncols int (default: 4)

Number of columns per row.

title str (default: None)

Title for the figure.

title_fontproperties Dict[Literal['size', 'weight'], str | int] (default: None)

Dictionary which should contain ‘size’ and ‘weight’ to define the fontsize and fontweight of the title of the figure.

share_legend bool (default: False)

Set a common legend when plotting multiple values, it will automatically scale if plotting continuous values like gene expression if vmax is not specified.

vmax float | str | None (default: None)

The value representing the upper limit of the color scale.

spacing tuple (default: (0.3, 0.2))

Spacing between subplots (height, width) padding between plots.

path str | PathLike[str] | Path (default: None)

Path to the folder to save the figure.

filename str (default: 'Umap.svg')

Name of file to use when saving the figure.

show bool (default: True)

If set to False, returns a dictionary with the matplotlib axes.

labels str (default: None)

Column in adata.obs with categorical values to add to the plot.

labels_fontproperties Dict[Literal['size', 'weight'], str | int] (default: None)

Dictionary which should contain ‘size’ and ‘weight’ to define the fontsize and fontweight of the labels.

labels_repel dict (default: None)

Additional arguments pass to adjust_text <https://adjusttext.readthedocs.io/en/latest/>_.

kwargs

Additional parameters pass to sc.pl.umap().

Return type:

None | Axes

Returns:

Depending on show, returns the plot if set to True or a dictionary with the axes.

Example

Visualize a categorical column

import dotools_py as do
adata = do.dt.example_10x_processed()
do.pl.umap(adata, 'annotation', split_by='condition', ncols=2, figsize=(9, 4), size=20)
do.pl.umap(adata, 'CD4', split_by='condition',  size=50, labels='annotation', cmap='Reds')

or the expression of a gene

do.pl.umap(adata, 'CD4', split_by='condition',  size=50, labels='annotation', cmap='Reds')