Scripts that were used to investigate the behaviour of the cytracepy distance function.
The presentation that was given can be found here.
This work was done with high velocity and therefore organization was an afterthought. If you are interested or tasked with rerunning this analysis please contact Duncan McColl, a former employee of the stuart lab.
In silico data was derived from the prossttYY trajectory model and given to us in a collaboration with Lucas Pinello's lab. Students and staff of the stuart lab can find the entire tar'd insilico directory on the 'tap' machine at /projects/sysbio/users/cellAtlas/data/insilico-trajectory.
For this experiment, sub samples of bifurcated tree trajectories were created and compared (see presentation for clearer explanation). That data can be found in this repo in data/13_data data/3_data.
The general idea and set up was to leverage the trajectory docker containers and bash to run off all the experiments. You can see the scripts in the /src directory that fire off the dockers. Use a python virtual env and the requirments.txt file to run the standalone python scripts.