text: user6621: 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
  
  
  user3631: 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).
  
original_text: 6621: <p>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?</p>
  <p>Update: the command line <code>object@commands</code> works perfectly for <code>...$FindClusters</code>. However, if I would like to find information about dimensions used there is an error:</p>
  <pre><code>...$FindNeighbors.SCT.pca Error in [[.Seurat(x, i, drop = TRUE) : Cannot find 'FindNeighbors.SCT.pca' in this Seurat object
  </code></pre>
   3631: <p>I am not sure of the output of <code>PrintFindClustersParams</code>, as I haven't use it before, but try with <code>object@commands</code>. It returns a list containing every command and parameters used.</p>
  <p>For example</p>
  <pre><code>...
  $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 
  ...
  </code></pre>
  <p>Re: update</p>
  <p>I think it depends on how you built the object. <code>FindNeighbors.SCT.pca</code> should be result of running <code>sctransform normalization</code>. If you use the <em>standard way</em>, you may have other names (e.g.<code>FindNeighbors.pca</code>).</p>
  