iclust {iCellR} | R Documentation |
This function takes an object of class iCellR and finds optimal number of clusters and clusters the data.
iclust( x = NULL, dist.method = "euclidean", k = 100, data.type = "pca", dims = 1:10, return.graph = FALSE )
x |
An object of class iCellR. |
dist.method |
the distance measure to be used to compute the dissimilarity matrix. This must be one of: "euclidean", "maximum", "mandatattan", "canberra", "binary", "minkowski" or "NULL". By default, distance="euclidean". If the distance is "NULL", the dissimilarity matrix (diss) should be given by the user. If distance is not "NULL", the dissimilarity matrix should be "NULL". |
k |
KNN the higher the number the less sensitivity, default = 100. |
data.type |
Choose between "tsne", "pca", "umap", default = "pca". |
dims |
PCA dimentions to be use for clustering, default = 1:10. |
return.graph |
return igraph object, default = FALSE. |
An object of class iCellR.