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fix the plot_control transcripts for large images #107
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This is partially fixed by bfd5957. Currently solved as follows (e.g. for VIZGEN): possibility to give crd when calculating transcript density:
the calculated transcript density for this crd is stored in the sdata object as an image layer (default name='transcript_density') (and in the .zarr file if backed by zarr). this layer can then be plotted by the
We should decide if we want to have a look at 'subsampeling by pulling location together' in the |
Fixed a bug in (commit ( c82c236 ))
the use of .unstack in:
did not automatically result in an image with dimensions similar as the other image layers, because not all rows or columns are populated with transcripts. Rewrote code to fix this + added option to sample transcripts before calculation of transcript density. Default behaviour is now that sampling is performed if number of transcripts inside the crd > 15 000 000.
One can also still provide a crd, and then sampling is not necessary:
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for the large image, too many rows need to be combined.
Maybe we can subsample, by pulling locations together, and creating sums over 25 pixels (5*5). This will reduce the plotting a lot.
Zoom-ins should be possible, we should put a threshold (or a hidden parameter) to state how big an image can be to still plot it fully!
Question: do we save this image in the object? I don't think that is necessary at the moment, but maybe there is a good reason to do so (i.g. visualization in napari)
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