First of all, thank you for your amazing project on CCI analysis.
While looking through details of cellphonedb implementation, I found small typo in description of radl percent analysis.
In cellphonedb/Docs/cluster_statistical_analysis_method_workflow.md (and cellphonedb/cellphonedb/src/core/methods/cpdb_statistical_analysis_helper.py), example of percent_analysis notes :
"""
Calculates the percents for cluster interactions and foreach gene interaction
If one of both is not 0 sets the value to 0. Else sets 1
EXAMPLE:
INPUT:
threshold = 0.1
cluster1 = cell1,cell2
cluster2 = cell3
cell1 cell2 cell3
ensembl1 0.0 0.6 0.3
ensembl2 0.1 0.05 0.06
ensembl3 0.0 0.0 0.9
interactions:
ensembl1,ensembl2
ensembl1,ensembl3
(after percents calculation)
cluster1 cluster2
ensembl1 0 0
ensembl2 1 1
ensembl3 1 0
RESULT:
cluster1_cluster1 cluster1_cluster2 cluster2_cluster1 cluster2_cluster2
ensembl1_ensembl2 (0,1)-> 0 (0,1)-> 0 (0,1)->0 (0,1)->0
ensembl1_ensembl3 (0,1)-> 0 (0,0)-> 1 (0,1)->0 (0,0)->1
"""
I believe
"""
(after percents calculation)
cluster1 cluster2
ensembl1 0 0
ensembl2 1 1
ensembl3 1 0
"""
should be
"""
(after percents calculation)
cluster1 cluster2
ensembl1 0 0
ensembl2 '0' '0'
ensembl3 1 0
"""
As percent calculations "Calculates the number of positive values and divides it for the total. If this value is < threshold, returns 1, else, returns 0".
Though implementation itself seems correct (following descriptions, not examples), I hope to know if this is actual typo in example (and hopefully correct them to prevent further confusion).
First of all, thank you for your amazing project on CCI analysis. While looking through details of cellphonedb implementation, I found small typo in description of radl percent analysis. In cellphonedb/Docs/cluster_statistical_analysis_method_workflow.md (and cellphonedb/cellphonedb/src/core/methods/cpdb_statistical_analysis_helper.py), example of percent_analysis notes : """ Calculates the percents for cluster interactions and foreach gene interaction If one of both is not 0 sets the value to 0. Else sets 1 EXAMPLE: INPUT: threshold = 0.1 cluster1 = cell1,cell2 cluster2 = cell3 cell1 cell2 cell3 ensembl1 0.0 0.6 0.3 ensembl2 0.1 0.05 0.06 ensembl3 0.0 0.0 0.9 interactions: ensembl1,ensembl2 ensembl1,ensembl3 (after percents calculation) cluster1 cluster2 ensembl1 0 0 ensembl2 1 1 ensembl3 1 0 RESULT: cluster1_cluster1 cluster1_cluster2 cluster2_cluster1 cluster2_cluster2 ensembl1_ensembl2 (0,1)-> 0 (0,1)-> 0 (0,1)->0 (0,1)->0 ensembl1_ensembl3 (0,1)-> 0 (0,0)-> 1 (0,1)->0 (0,0)->1 """
I believe """ (after percents calculation) cluster1 cluster2 ensembl1 0 0 ensembl2 1 1 ensembl3 1 0 """ should be """ (after percents calculation) cluster1 cluster2 ensembl1 0 0 ensembl2 '0' '0' ensembl3 1 0 """ As percent calculations "Calculates the number of positive values and divides it for the total. If this value is < threshold, returns 1, else, returns 0".
Though implementation itself seems correct (following descriptions, not examples), I hope to know if this is actual typo in example (and hopefully correct them to prevent further confusion).