Label-free mode?

[amoore-vm]

In the CellChat publication and documentation, it mentions a label-free model: "CellChat requires two user inputs: one is the gene expression data of cells, and the other is either user assigned cell labels (i.e., label-based mode) or a low-dimensional representation of the single-cell data (i.e., label-free mode). For the latter, CellChat automatically groups cells by building a shared neighbor graph based on the cell-cell distance in the low-dimensional space or the pseudotemporal trajectory space. "

We are getting poor results on Xenium data (20 ligand-receptor pairs). We would like to try using the label-free mode, but the tutorial assumes you will provide labeled data. How do you run label-free mode?

[sqjin]

@amoore-vm The Xenium data is single-cell resolution, and I suggest to perform cell annotation by yourself. Because there are few signaling genes, you can skip the step of 'identifyOverExpressedGenes'