Merge current development branch #70
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Moving over the faster PPA script and the cn_map function that shows a more detailed legend.
This function allows to generate the catplot but with the actual masks instead of just the centroids.
The figsize can be adjusted again however we might need to check the placing of the legend label
This bug caused differences in the results if the comparison was drawn in different directions
…f cell types that can shift the results
Updating the text removing old names
- adding interactive clustering function - fixing cell-cell distance analysis
- allowing python 3.10 - adding panel for interactive clustering
- adding missing docs - removing unused functions
- add a new option to compress images - add a new function to use TM as catplot alternative
- add filter for rare cell types - update notebook
- based on notebook 3 - Includes GUI demo for users to try - Includes screenshot with example
- added chuck wise processing of the dataset if more than 16GB are required - pairwise distances are calculated in chunks of 1000 - removal of odd function name replaced with better name
script allows to adjust the install according to machine and OS
- avoid issues if users try to use PPA and have a region with only one structure
Remove windows related features from install script
- This feature is yet untested - This feature still needs a python test function - use at own risk
…d make the scatterplots optional, add docker files
- Fixed Mac and Windows instructions
- Allow for automatic install of plug-ins - Add TM catplot to TM notebook
…o combined_updates_yuqi
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