run clumppling — gt_clumppling • tidygenclust

This function runs the clumppling algorithm.

gt_clumppling(
  input_path,
  input_format = "admixture",
  cd_param = 1,
  use_rep = 0,
  merge_cls = 0,
  cd_default = 1,
  output_path = tempfile("clump_out")
)

Arguments

input_path: the path where the Q files are stored, either a directory or a zip archive, or a q_matrix_list object
input_format: a string defining the format of the input files, one of 'admixture' (default)
cd_param: the cd_param use_rep boolean on whether a representative repeat should be used as a consesus for a mode. Defaults to FALSE, which leads to the computatoin of an average
use_rep: boolean
merge_cls: boolean,
cd_default: boolean
output_path: (optional) the clumppling functions in python save everything to file. By default, R stores the information in objects in the environment, and sends those files to a temporary directory that will be cleared at the end of a session. output_path allows to change the location of those files. This is only useful to those interested in recovering the same files as created by the python clumppling module, or for debugging.

Value

a list of class clumpling TODO describe the elements of the list

Details

If you would like to generate an annotated autoplot from your gt_clumppling object, ensure that all individuals from the same population are adjacent to one another in the Q-matrix or gt_admix object supplied to gt_clumppling. Autoplot 'group' argument requires that all individuals from the same group are adjacent.