Supplementary Figures #59
Description
For now, this can be a place to collect supplementary figure ideas. Later, can become the parent issue for making supplementary figures.
SF1
Need a Supp figure and table that shows the current state of the project ie modules and recipes. Two simple boxes with labelled sup-boxes should suffice and the table with columns such as GitHub repo link, version, zenodo DOI, etc.
SF2
- ATAC has multiple regions per gene that are shown as markers → show gene tracks for those
- adjacency matrices for crossprediction network plots
(@sreichl I decided to put this here instead of the manuscript draft since it feels easier to coordinate here)
SF3
- decreasing correlation in differentiated cells
- ad TF analysis: GMP would be "in the middle" of the differentiation trajectory and I would assume that the "Convergent" genes are enriched in the TFBS motifs that we find for HSC EP and Mono TA
Consider adding interesting processing plots into main figure or as supplements
RB
- I see the point of showing only final results in the main figures
- but MrBiomics does really cool processing, e.g., the spilterlize module CFA plots or other unsupervised plots e.g., clustering → this is a main advantage point for me, going beyond making UMAPs only
- not sure what would make sense: I will for now stick to the original plan and we can move around things later
SR
Totally agreed, good that you document it here. Focus is on plots that we require to show the reader, both in the paper and the poster. But then we have to highlight the unique selling points as well, ideall in a very comprehensive but visually appealing way in main figures or in the text + supplementary.