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 )
2d object to add
meta cell id to work with
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 of the metacell graph to use. If this is null the function will compute an mgraph itself using the cell graph
determine if mismatch in mc names are to be ignored.
gene set name for use in parametric graph and/or umap 2d projection
list of genes to exclude from the features gene set
if this is True, mc edges will be determined using parametric distances and not the cells k-nn graph.
the location parametr of the logistic function used to determine parametric distances between metacelles
the lscale parametr of the logistic function used to determine parametric distances between metacelles
should the mc confusion matrix be symmetrized before computing layout?