This function executes a ubuntu docker that produces a specific number of permutation to evaluate clustering.

```
clusterStability(
group = c("sudo", "docker"),
scratch.folder,
file,
nPerm,
range1 = 3,
range2 = 3,
separator,
logTen = 0,
clustering,
perplexity = 10,
pcaDimensions,
seed = 1111
)
```

## Arguments

- group,
a character string. Two options: sudo or docker, depending to which group the user belongs

- scratch.folder,
a character string indicating the path of the scratch folder

- file,
a character string indicating the path of the file, with file name and extension included

- nPerm,
number of permutations to perform the pValue to evaluate clustering

- range1,
first number of cluster for k means algorithm

- range2,
last number of cluster for k means algorithm

- separator,
separator used in count file, e.g. '\t', ','

- logTen,
1 if the count matrix is already in log10, 0 otherwise

- clustering,
clustering method to use : "SIMLR" , "tSne", "griph"

- perplexity,
Number of close neighbors for each point. This parameter is specific for tSne. Default value is 10.Setting this parameter when use a clustering method different by tSne will be ignored.

- pcaDimensions,
dimensions to use for pca reduction for Seurat

- seed,
important value to reproduce the same results with same input

## Value

plot with cluster stability

## Author

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino