Metacell layout using force directed projection of a low degree mc graph

mcell_mc2d_force_knn(
  mc2d_id,
  mc_id,
  graph_id,
  mgraph_id = NULL,
  ignore_mismatch = F,
  symmetrize = F,
  ignore_edges = NULL,
  feats_gset = NULL,
  feats_exclude = NULL,
  graph_parametric = F,
  logist_loc = 1,
  logist_scale = 0.2,
  logist_eps = 0.00004,
  max_d_fold = 3,
  use_umap_for_2d_pos = F,
  umap_mgraph = F,
  uconf = NULL
)

Arguments

mc2d_id: 2d object to add
mc_id: meta cell id to work with
graph_id: graph_id of the similarity graph on cells from the metacell. This should always be specified, even if an mgraph is supplied since we use the obejct to position cells releative to metacels
mgraph_id: mgraph_id of the metacell graph to use. If this is null the function will compute an mgraph itself using the cell graph
ignore_mismatch: determine if mismatch in mc names are to be ignored.
feats_gset: gene set name for use in parametric graph and/or umap 2d projection
feats_exclude: list of genes to exclude from the features gene set
graph_parametric: if this is True, mc edges will be determined using parametric distances and not the cells k-nn graph.
logist_loc: the location parametr of the logistic function used to determine parametric distances between metacelles
logist_scale: the lscale parametr of the logistic function used to determine parametric distances between metacelles
symetrize: should the mc confusion matrix be symmetrized before computing layout?