Tree-based mapping — map_dend • scrattch.mapping

Returns the mapping membership of each cell to each node and leaf using a tree-based method. This is a wrapper function for map_dend.

map_dend(
  dend,
  cl,
  dat,
  map.dat,
  select.cells,
  p = 0.8,
  low.th = 0.2,
  default.markers = NULL
)

Arguments

dend: dendrogram for mapping
cl: factor indicating which cluster each cell type is actually assigned to in the reference data set
dat: normalized data of the REFERENCE data set
map.dat: normalized data of the MAPPING data set. Default is to map the data onto itself.
p: proportion of marker genes to include in each iteration of the mapping algorithm.
low.th: the minimum difference in Pearson correlation required to decide on which branch to map to. otherwise, a random branch is chosen.
default.markers: not used

Value

a matrix of confidence scores (from 0 to 100) with rows as cells and columns as tree node/leafs. Values indicate the fraction of permutations in which the cell mapped to that node/leaf using the subset of cells/genes in map_dend