Tree-based mapping — rfTreeMapping • 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. Includes Minor adjustments from the function of the same name in mfishtools.

rfTreeMapping(
  dend,
  refDat,
  clustersF,
  mapDat = refDat,
  p = 0.7,
  low.th = 0.15,
  bootstrap = 100,
  seed = 1
)

Arguments

dend: dendrogram for mapping
refDat: normalized data of the REFERENCE data set
clustersF: factor indicating which cluster each cell type is actually assigned to in the reference data set
mapDat: 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.
bootstrap: Number of bootstrapping runs to calculate the membership from (default = 100)
seed: added for reproducibility

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