Tree based mapping — treeMap • scrattch.mapping

Tree based mapping

treeMap(
  AIT.anndata,
  query.data,
  p = 0.8,
  low.th = 0.1,
  bootstrap = 100,
  genes.to.use = rep(TRUE, dim(AIT.anndata)[2]),
  seed = 1
)

Arguments

AIT.anndata: A reference taxonomy anndata object.
query.data: A logCPM normalized matrix to be annotated.
p: The proportion of marker genes to include in each iteration of the mapping algorithm.
low.th: The minimum difference in Pearson correlation to the reference cluster mean gene expression between the top-matched cluster and others. If the difference is higher than low.th, the mapping process continues; otherwise, a random branch is chosen.
bootstrap: Number of bootstrapping runs to calculate the membership from (default = 100)
genes.to.use: The set of genes to use for tree mapping (default is all marker genes in the tree). Can be (1) a character vector of gene names, (2) a TRUE/FALSE (logical) vector of which genes to include, or (3) a column name in AIT.anndata$var corresponding to a logical vector of variable genes. If anything is provided the set of genes used is the intersection of all marker genes and the gene set here.
seed: Value of the seed for reproducibility

Tree mapping results as a data.frame.