unravel.allen_institute.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:

abca_merfish_filter and merfish_join_expression_data.py
Or: RNAseq_expression.py and RNAseq_filter.py

Outputs:

path/input_sunburst_expression_thr<value>.csv, input_mean_expression_lut.txt, and input_percent_expression_thr<value>_lut.txt

Note

LUT location: unravel/core/csvs/ABCA/WMB_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]

unravel.allen_institute.abca.sunburst.sunburst_expression.parse_args()[source]#

unravel.allen_institute.abca.sunburst.sunburst_expression.main()[source]#