Question: How can i control the cluster number in scRNASeq clustering by Seurat package
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gravatar for wenchuan.xie
13 months ago by
wenchuan.xie10
wenchuan.xie10 wrote:

Hi all, I analysised the 10x dataset by Seurat pkg, when i used the TSNEPlot function to plot the TSNE plot of clustering result, i found the number of cluster always different. How can i control the cluster number? which function or parameters i can use to limit the cluster number. enter image description here

seurat single cell rna-seq • 2.6k views
ADD COMMENTlink modified 13 months ago by igor9.5k • written 13 months ago by wenchuan.xie10
0
gravatar for igor
13 months ago by
igor9.5k
United States
igor9.5k wrote:

When you run FindClusters(), you specify a resolution. This will determine the number of clusters.

From the PBMC tutorial:

The FindClusters function implements the procedure, and contains a resolution parameter that sets the ‘granularity’ of the downstream clustering, with increased values leading to a greater number of clusters. We find that 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. The clusters are saved in the object@ident slot.

ADD COMMENTlink written 13 months ago by igor9.5k
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