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Refine clustering

In the previous exercise, we used the default parameters of the function FindClusters() and did not find the same clustering as in the mouse epithelium published paper. Let's look at the result of the clustering when the clustering parameters are different:

seuset <- FindClusters(
    object = seuset, 
    reduction.type = "pca", 
    dims.use = 1:10, 
    resolution = 1.8, 
    print.output = FALSE
)

We can now compare again our clustering to the clustering from the published mouse epithelium paper:

pub <- seuset@meta.data[, "publishedClusters"]
table(seuset@ident, pub)

The output is as follows:

   published
     7  9 15
  0  0 45  1
  1 41  1  0
  2  0  0  6

Is our new clustering the same as the clustering from the mouse epithelium paper?

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