sparrow.pl.transcript_density

sparrow.pl.transcript_density#

sparrow.pl.transcript_density(sdata, img_layer=['raw_image', 'transcript_density'], channel=0, crd=None, figsize=None, output=None)#

Visualize the transcript density layer.

This function wraps around the plot_shapes function to showcase transcript density.

Parameters:

  • sdata (SpatialData) – Data containing spatial information for plotting.

  • img_layer (tuple[str, str] (default: ['raw_image', 'transcript_density'])) – A tuple where the first element indicates the base image layer and the second element indicates the transcript density.

  • channel (int (default: 0)) – The channel of the image to be visualized. If the channel not in one of the images, the first available channel of the image will be plotted

  • crd (Optional[tuple[int, int, int, int]] (default: None)) – The coordinates for the region of interest in the format (xmin, xmax, ymin, ymax). If None, the entire image is considered, by default None.

  • figsize (Optional[tuple[int, int]] (default: None)) – The figure size for the visualization. If None, a default size will be used.

  • output (Union[str, Path, None] (default: None)) – Path to save the output image. If None, the image will not be saved and will be displayed instead.

Return type:

None

Returns:

: None

Examples

>>> sdata = SpatialData(...)
>>> transcript_density(sdata, img_layer=["raw_img", "density"], crd=(2000,4000,2000,4000))

See also

sparrow.im.transcript_density

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