Plotting only transcripts


is there a simple way to use Squidpy to only plot transcripts? I would like to plot the raw transcripts without knowing to which cell they belong and toggle between genes for visualisation purposes only.


In case I understand your question correctly, you could use the render_points() function of the spatialdata-plot library after converting your data to the spatialdata format

Thx! Will have a look into it.

Is there any tutorial on how to populate a SpatialData object? Specifically I fail to import my transcripts with the add_points() method.

Getting this error: ValueError: :attr:dask.dataframe.core.DataFrame.attrs does not contain transform.

Not sure, if this is dask version issue or my input data frame is in the wrong shape/dtype.

Hey, sorry for the late reply! Didn’t see the notification.

Which data are you using? Over at GitHub - scverse/spatialdata-io we provide readers for most technologies which should make it easier to get your data into the required format.