Array trapping efficiency, confluence, and single cell initial conditions

[eric-czech]

Hey @jmotschman ,

I added some things to make it possible to scope all the analysis (including the app) to only apartments that started with single cells. It's not a real-time toggle that you can easily exclude yet, but I'll work that in if it comes up a lot. After pulling down these changes, all growth rates will be ignored by default unless they were computed for apartments that started with single cells.

Otherwise, I also added a command to generate notebooks that contain visualizations like this:

• Growth rate heatmaps (with no single cell requirement):

celldom run-array-analysis \
--experiment-config-path=/lab/repos/celldom/config/experiment/experiment_example_G3.yaml \
--output-dir=/lab/data/celldom/output/20180923-G3-full \
--apartment-initial-conditions=None \
--na-growth-rate-fill-value=0 

• Growth rate heatmaps (ignoring apartments that didn't start with a single cell):

celldom run-array-analysis \
--experiment-config-path=/lab/repos/celldom/config/experiment/experiment_example_G3.yaml \
--output-dir=/lab/data/celldom/output/20180923-G3-full \
--apartment-initial-conditions='single_cell' \
--na-growth-rate-fill-value=None

• Single cell trapping efficiency estimates:

• Locations of apartments in "confluence":

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Those are all things that end up in the notebook that gets generated so you could also open it in JupyterLab and start editing some of the graphing properties if you wanted to. There's not an easy way to do that all as plotly figures that work well within a notebook (so opening the plot in their online editor wouldn't be an option) but if you give me a sense of what kinds of things you'd want to change about the visualizations, I'll find some way to make that as easy as possible.