supervised method about cytocommunity HOT 3 CLOSED

Hi,
Please see the "CellTypeEnrichmentAnalysis.zip" just uploaded to the master branch.
It includes example Matlab scripts for cell type enrichment analysis of the identified TCNs by unsupervised CytoCommunity.
You can put it in the same directory with the folders Step1/2/3/4_Output. Just modify the hyperparameters in the gen_CellTypeEnrichmentMatrix.m and run it. You can obtain a CellTypeEnrichment_Res.mat file, which includes a matrix named "CellTypeByTCN_EnrichScoreMatrix" with rows representing cell types same as in the "/Step1_Output/UniqueCellTypeList.txt" and columns representing TCNs from TCN-1 to TCN-M. The value in the matrix is -log10(hypergeometric test p-value). This script can be easily adapted to analyzing results of the supervised version.

from cytocommunity.

Thank you

Please explain how to get the additional file for the supervised approach.

from cytocommunity.

Additional "**_GraphLabel.txt" files are prepared based on your dataset. For example, if your dataset includes samples of two conditions, you can put an integer "0" in the "GraphLabel.txt" of the samples of condition-1 and an integer "1" for the samples of condition-2. Example files can be found under the directory "Tutorial/Supervised/MIBI-TNBC_Input/".

from cytocommunity.