How can I select cluster for neighborhood analysis?

[DrZing]

Hi,

I'm trying to run the neighborhood analysis, and I'm wondering if I can only select the wanted clusters from the phenograph results.

Thank,
Zing

[DenisSch]

Dear Zing,
Yes, this is possible. Instead of manual gating, you can just "merge" unwanted PhenoGraph clusters before the analysis. Afterwards please follow the steps in the documentation:

4. Custom clustering
   The custom clustering enables the user to combine an unsupervised clustering method
   (PhenoGraph) with previous knowledge (manual gating) about the data. This function was added
   with version 1.73. The result of a PhenoGraph run sometimes does not separate a very specific
   cluster of cells, which is of interest to the user. To enforce the assignment of this group of cells to a
   separate cluster, you can manually gate on one or multiple cell populations, as described above.
   Select the resulting gate(s) from the samples list box and start the “Custom Clustering” from the
   “Sample Options” drop-down menu. The subgroups of cells in the selected gates will be considered
   individual clusters, while the rest of the cells, not contained in any of the selected clusters, will be
   assigned to the clusters of a previous PhenoGraph run. To distinguish the custom clusters from the
   PhenoGraph clusters, the user-defined clusters are named in steps of hundreds (first custom cluster
   = Cluster 100, second custom cluster = Cluster 200, …). Please find further details in the
   corresponding publication (Schulz et al., 2017).