This tool aligns the CCA subspaces and performs integrated analysis on the data; t-SNE. clustering and visualisation of the clusters. This tool can be used for two sample combined Seurat objects.
As inputs, give the combined Seurat object generated with "Seurat Combine two samples and perform CCA" tool.
The resolution parameter sets the 'granularity' of the downstream clustering, with increased values leading to a greater number of clusters. Setting this parameter between 0.6-1.2 typically returns good results for single cell datasets of around 3K cells. Optimal resolution often increases for larger datasets -use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities.
The number of CCs to use need to be decided by the user based on the CCAplots from the Seurat CCA -tool.
For more details, please check the Seurat tutorials for multiple sample analysis.