unravel.abca.sunburst.sunburst_expression module#
Use abca_sunburst_expression or sbe from UNRAVEL to calculate mean expression for all cell types in the ABCA and make a sunburst plot.
- Prereqs:
merfish_filter.py and merfish_join_expression_data.py
Or: RNAseq_expression_in_mice.py and RNAseq_filter.py
Note
LUT location: unravel/core/csvs/ABCA/ABCA_sunburst_colors.csv
- Next steps:
Use input_sunburst.csv to make a sunburst plot or regional volumes in Flourish Studio (https://app.flourish.studio/)
It can be pasted into the Data tab (categories columns = cell type columns, Size by = percent column)
Preview tab: Hierarchy -> Depth to 5, Colors -> paste content of …_colors.csv into Custom overrides
Usage:#
abca_sunburst_expression -i path/VTA_DA_cells_Th_expression.csv -g gene [-o path/out_dir] [-n] [-v]