unravel.allen_institute.abca.sunburst.sunburst module#

Use abca_sunburst or sb from UNRAVEL to generate a sunburst plot of cell type proportions across all ontological levels.

Prereqs:

  • merfish_filter.py or RNAseq_expression.py + RNAseq_join_expression_data.py to generate the input cell metadata.

Outputs:

  • path/input_sunburst.csv and [WMB_sunburst_colors.csv or HMB_sunburst_colors.csv if –output_lut is provided]

Note

  • LUT location: unravel/core/csvs/ABCA/

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 hex codes from …_sunburst_colors.csv into Custom overrides

Usage:#

abca_sunburst -i path/cell_metadata_filtered.csv [-n] [-l] [-v]

unravel.allen_institute.abca.sunburst.sunburst.parse_args()[source]#
unravel.allen_institute.abca.sunburst.sunburst.filter_non_neuronal_cells(cells_df, species)[source]#

Filter out non-neuronal cells based on the species.

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