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 abca_merfish_join_expression

  • Or: abca_scRNAseq_expression and abca_scRNAseq_filter

Outputs:

  • path/input_sunburst.csv

  • path/sunburst_expression_thr<value>/input__gene-GENE_sunburst_expression_thr<value>.csv

  • path/mean_expression_lut/input__gene-GENE_mean_expression_lut.txt

  • path/percent_expression_thr<value>_lut/input__gene-GENE_percent_expression_thr<value>_lut.txt

  • path/all_expression_thr<value>/input__gene-GENE_all.csv

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

  • abca_sunburst_expression_overview to summarize mean and percent expression for all cells and each cell type.

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]#