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How can i control the cluster number in scRNASeq clustering by Seurat package
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17 months ago

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

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20 months ago
igor 7.7k
United States

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.

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