Clustering information saved in Seurat object Seurat V2 had a option to find clustering information saved in object: PrintFindClustersParams(object = pbmc). How can I get the same clustering parameters from objects in Seurat3? Do I need to manually save clustering parameters or they are saved automatically?
Update: the command line object@commands works perfectly for ...$FindClusters. However, if I would like to find information about dimensions used there is an error:
...$FindNeighbors.SCT.pca Error in [[.Seurat(x, i, drop = TRUE) : Cannot find 'FindNeighbors.SCT.pca' in this Seurat object
I am not sure of the output of PrintFindClustersParams, as I haven't use it before, but try with object@commands. It returns a list containing every command and parameters used.
For example
...
$FindNeighbors.SCT.pca
Command: FindNeighbors(seurObj, dims = 1:20, verbose = vrb)
Time: 2019-12-11 12:41:12
reduction : pca 
dims : 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
assay : SCT 
k.param : 20 
compute.SNN : TRUE 
prune.SNN : 0.06666667 
nn.method : rann 
annoy.metric : euclidean 
nn.eps : 0 
verbose : FALSE 
force.recalc : FALSE 
do.plot : FALSE 
graph.name : SCT_nn SCT_snn 

$FindClusters
Command: FindClusters(seurObj, verbose = vrb)
Time: 2019-12-11 12:41:17
graph.name : SCT_snn 
modularity.fxn : 1 
resolution : 0.8 
algorithm : 1 
n.start : 10 
n.iter : 10 
random.seed : 0 
group.singletons : TRUE 
verbose : FALSE 
...

Re: update
I think it depends on how you built the object. FindNeighbors.SCT.pca should be result of running sctransform normalization. If you use the standard way, you may have other names (e.g.FindNeighbors.pca).