<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>

CC BY-SA 4.0
2019-12-11T13:58:37.977Z
2021-05-05T06:31:19.620Z
2021-05-05T06:31:19.620Z
fra
<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>

<seurat><single-cell><clustering>
Clustering information saved in Seurat object
# Clustering information saved in Seurat object

(Asked by: username_0 on 2019-12-11)

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

**Tags:** seurat, single-cell, clustering

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## 1 answers

### Answer by username_1 on 2019-12-11. Score: 1

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).


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