A text file containing the gene modules is written to the Antler output folder.
| name | character string. The name of the cell clusters object. Multiple cell clusters objects under different names can be stored. |
|---|---|
| gene_modules_name | character string. The name of the list of gene modules from which the cell-to-cell distance will be calculated. |
| method | character string. The clustering method to use. Currently only |
| cell_cell_dist | numeric matrix. Optionally a matrix containing the cell-to-cell distances can be provided. If NA (default), the matrix is calculated internally using Euclidean distance. |
| logscaled | logical. If TRUE (default), the gene expression level are log-transformed and z-normalized before calculating the cell-to-cell distance. If FALSE, no transformation is applied to the levels. |
| num_clusters | an integer value indicating the number of cell clusters. If NULL (default) a heuristic method is used to find the optimal number of clusters. |
| data_status | character string. Specifies whether the gene expression levels to be used are raw ("Raw"), normalized ("Normalized") or have been imputed ("Smoothed"). Default to "Normalized". |
| process_plots | a logical value indicating whether to render the heuristic trade-off determining the number clusters. Default to FALSE. |