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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
69 stars 25 forks source link

Default plotting settings for all plots #206

Open ngreenwald opened 3 years ago

ngreenwald commented 3 years ago

Is your feature request related to a problem? Please describe. Each plot uses a different set of parameters for key features like font size, colormap, line color, etc.

Describe the solution you'd like A default for the most important plotting options that can be used for all functions. These should be optimized to look nice, and put in a dedicated matplotlib/seaborn/whatever parameters file, which can be imported.

ngreenwald commented 1 year ago

More concretely, we should come up with a core set of color maps that people really like. I think doing some user polling to see what Erin, YeEun, Meelad, Bryan, Inna, Erin Soon, etc have used before would be good.

It would be great to collect the colormaps that people have used for heatmaps, gradients, and categorical data (split by how many unique categories there were).

We can then aggregate them, but together an overview doc, and see which ones everyone in the lab/Mike likes the most. Then make them the default plotting scheme, as well as easily importable