unravel.cluster_stats.prism module#

Use cstats_prism (prism) from UNRAVEL to organize data for clusters for plotting in Prism.

Inputs:

*.csv from cstats_org_data (in working dir) or cstats_mean_IF

CSV naming conventions:

  • Condition: first word before ‘_’ in the file name (use utils_prepend if needed)

  • Sample: second word in file name

Example unilateral inputs:

  • condition1_sample01_<cell|label>_density_data.csv (columns: sample, cluster_ID, <cell_count|label_volume|mean_IF_intensity>, [cluster_volume], [cell_density|label_density], …)

  • condition1_sample02_<cell|label>_density_data.csv

  • condition2_sample03_<cell|label>_density_data.csv

  • condition2_sample04_<cell|label>_density_data.csv

Example bilateral inputs (if any file has _LH.csv or _RH.csv, the command will attempt to pool data):

  • condition1_sample01_<cell|label>_density_data_LH.csv

  • condition1_sample01_<cell|label>_density_data_RH.csv

Columns in the input .csv files:

sample, cluster_ID, <cell_count|label_volume|mean_IF_intensity>, [cluster_volume], [cell_density|label_density], …

Outputs:

  • Outputs saved in ./cluster_validation_summary/

  • Cluster order follows -ids order

  • <cell_count|label_volume|mean_IF_intensity>_summary.csv

  • [<cell_density|label_density>_summary.csv]

  • [<cell_density|label_density>_summary_across_clusters.csv]

  • [cluster_volume_summary.csv]

Note

  • cstats_table saves valid_clusters_dir/valid_cluster_IDs_sorted_by_anatomy.txt

Usage:#

cstats_prism [-ids 1 2 3] [-p /path/to/csv/files/from/cstats_validation_or_cstats_mean_IF] [-v]

unravel.cluster_stats.prism.parse_args()[source]#
unravel.cluster_stats.prism.sort_samples(sample_names)[source]#
unravel.cluster_stats.prism.generate_summary_table(csv_files, data_column_name)[source]#
unravel.cluster_stats.prism.main()[source]#