search

WayScience / phenotypic_profiling

Machine learning for predicting 15 single-cell phenotypes from cell morphology profiles
Creative Commons Attribution 4.0 International
2 stars 3 forks source link

Add JUMP Mitocheck feature analysis comparison with KS tests #42

Closed gwaybio closed 1 year ago

gwaybio commented 1 year ago

Related to the analysis in https://github.com/WayScience/JUMP-single-cell/pull/13

jump_mitocheck_feature_space_analysis

Legend: Comparing JUMP and Mitocheck nuclei feature spaces. (A) Kolmogorov-Smirnov (KS) test results comparing JUMP and Mitocheck per common CellProfiler feature colored by specific CellProfiler feature group. The boxplot whiskers represent the interquartile range of 1,000 permutations of randomly subsampled JUMP single-cells from a single plate (JUMP Pilot plate BR00116991) compared to Mitocheck. Mitocheck and JUMP sample size is the same (n = 2,916). We show both raw and z-score normalized comparisons. (B) The same KS test results focused on AreaShape measurements, which showed the lowest differences in feature distributions across datasets. (C) Comparing variance of JUMP and Mitocheck for all CellProfiler features. The dotted lines are the function y=x (anything below is a feature with higher variance in Mitocheck). Note that low variance features group together near zero and obscure colors. (D) The same variance plot as panel C except focused only on the AreaShape features.

review-notebook-app[bot] commented 1 year ago

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

gwaybio commented 1 year ago

Thanks again for the review @jenna-tomkinson ! I will go ahead and merge now.