unravel.region_stats.rstats_summary module#

Use rstats_summary (rss) from UNRAVEL to plot cell densensities for each region and summarize results.

Inputs:

  • CSVs with cell densities for each region (e.g., regional_stats/<condition>_sample??_cell_densities.csv)

  • Input CSV columns: Region_ID, Side, ID_Path, Region, Abbr, <OneWordCondition>_sample??

  • The <OneWordCondition>_sample?? column has the cell densities for each region.

Outputs:

  • Saved to ./<args.test_type>_plots_<side>

  • Plots for each region with cell densities for each group (e.g., Saline, MDMA, Meth)

  • Summary of significant differences between groups

  • regional_cell_densities_all.csv (Columns: columns: Region_ID,Side,Name,Abbr,Saline_sample06,Saline_sample07,…,MDMA_sample01,…,Meth_sample23,…)

Note

  • Example hex code list (flank arg w/ double quotes): [‘#2D67C8’, ‘#27AF2E’, ‘#D32525’, ‘#7F25D3’]

  • Default csv: UNRAVEL/unravel/core/csvs/CCFv3-2020_regional_summary.csv

  • It has columns: Region_ID, ID_Path, Region, Abbr, General_Region, R, G, B

  • Alternatively, use CCFv3-2017_regional_summary.csv or provide a custom CSV with the same columns.

Usage for Tukey tests:#

rstats_summary –groups Saline MDMA Meth -hemi both [-div 10000] [-y cell_density] [-csv CCFv3-2020_regional_summary.csv] [-b ABA] [-s light:white] [-o tukey_plots] [-e pdf] [-v]

Usage for t-tests:#

rstats_summary –groups Saline MDMA -hemi both -t t-test -c Saline [-alt two-sided] [-div 10000] [-y cell_density] [-csv CCFv3-2020_regional_summary.csv] [-b ABA] [-s light:white] [-o t-test_plots] [-e pdf] [-v]

unravel.region_stats.rstats_summary.parse_args()[source]#
unravel.region_stats.rstats_summary.get_region_details(region_id, df)[source]#
unravel.region_stats.rstats_summary.parse_color_argument(color_arg, num_groups, region_id, csv_path)[source]#
unravel.region_stats.rstats_summary.summarize_significance(test_df, id)[source]#

Summarize the results of the statistical tests.

Parameters:

  • test_df (-) – the DataFrame containing the test results (w/ columns: group1, group2, p-value, meandiff)

  • id (-) – the region or cluster ID

Returns:

the DataFrame containing the summarized results

Return type:

  • summary_df (DataFrame)

unravel.region_stats.rstats_summary.process_and_plot_data(df, region_id, region_name, region_abbr, side, out_dir, group_columns, args)[source]#
unravel.region_stats.rstats_summary.main()[source]#