unravel.cluster_stats.find_incongruent_clusters module

Use cstats_find_incongruent from UNRAVEL if cstats_fdr was used to convert non-directional p value maps into directional cluster indices. This helps to find clusters where the direction of the mean intensity difference between groups does not match direction of the difference in cell/label density between groups.

Input:

• ./_cluster_validation_info/tukey_results.csv or ttest_results.csv from cstats

• Columns: ‘cluster_ID’, ‘comparison’, ‘higher_mean_group’, ‘p-value’, ‘significance’

Output:

• Cluster IDs where the mean intensity difference does not match the density difference between groups A and B.

Note

• This is modules is useful to find clusters where z-scoring introduces incongruencies between the mean intensity difference and the density difference.

• For example, if group A has increased IF in region A and not B, z-scoring may decrease the relative intensity of region B.

• This decrease for region B for one group, may introduce a difference in the mean intensity between groups that is not reflected in the density difference.

Usage:

cstats_find_incongruent -c tukey_results.csv -l groupA -g groupB [-v]

unravel.cluster_stats.find_incongruent_clusters.parse_args()

unravel.cluster_stats.find_incongruent_clusters.find_incongruent_clusters(df, expected_lower_mean_group, expected_higher_mean_group)

unravel.cluster_stats.find_incongruent_clusters.main()