mcell_mc2d_force_knn: Metacell layout using force directed projection of a low...

In tanaylab/metacell: Meta cell analysis for single cell RNA-seq data

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

Description

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

Usage

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?

tanaylab/metacell documentation built on Jan. 29, 2025, 1:34 a.m.