dotools_py.pl.layers

dotools_py.pl.layers(adata, color, key_layers, ncols=4, normalise=False, show=True, figsize=(15, 8), path=None, filename='Layers.pdf', **kwargs)

Plot several layers.

Plot different layers in subplots. Useful for deconvolution analysis with celltype counts in layers.

Parameters:

adata AnnData

annotated data matrix.

color str

var_names or obs column to plot.

key_layers str | list

layers to plot.

ncols int (default: 4)

number of columns in the plot.

normalise bool (default: False)

do log-normalization on the layers.

show bool (default: True)

if set to False, return axis.

figsize tuple (default: (15, 8))

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

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

Path to the folder to save the figure.

filename str (default: 'Layers.pdf')

Name of file to use when saving the figure.

kwargs

additional arguments for sc.pl.spatial.

Return type:

None | Axes

Returns:

None or plt.axes.

Examples

import dotools_py as do
adata = do.dt.example_visium_processed()
do.pl.layers(adata, "NPPA", key_layers= ['counts', 'logcounts'], img_key="lowres")