Hello everyone, I am working on a scRNA-Seq data with multiple clustering algorithms. I want to see the quality of clustering with Silhouette plot function of "cluster" package. As I know, the function requires a distance matrix. Now my data is stored in Seurat object (can be transformed to SingleCellExperiment) and clustering with Seurat method provides an SNN matrix. Which option would be better to use?
1) Using SNN matrix as distance matrix
2) Calculating a new distance matrix with dist() function. (Actually I tried with Euclidead distance but did not work. Plots look amazingly low quality). My data is really big so I am sure it will take so much time. I can create the distance matrix with principle components (let's say first 50 PCs).
Thank you in advance.