distTreeMapping: (Euclidean) distance mapping

In AllenInstitute/mfishtools: Building Gene Sets and Mapping mFISH Data

(Euclidean) distance mapping

Description

Returns the distance between expression of each cell and representative value for each node and leaf (default is based on euclidean distance). In our hands this is does not work very well.

Usage

distTreeMapping(
  dend = NA,
  refDat = NA,
  mapDat = refDat,
  medianDat = NA,
  clusters = NA,
  genesToMap = rownames(mapDat),
  returnSimilarity = TRUE,
  use = "p",
  ...
)

Arguments

dend	dendrogram for mapping. Ignored if medianDat is passed
refDat	normalized data of the REFERENCE data set. Ignored if medianDat is passed
mapDat	normalized data of the MAPPING data set. Default is to map the data onto itself.
medianDat	representative value for each leaf and node. If not entered, it is calculated
clusters	cluster calls for each cell. Ignored if medianDat is passed
genesToMap	which genes to include in the correlation mapping
returnSimilarity	FALSE to return distance, TRUE to return something like a similarity
use, ...	additional parameters for dist (for back-compatiblity; doesn't work)

Value

matrix of Euclidean distances between cells (rows) and clusters (columns)

AllenInstitute/mfishtools documentation built on July 5, 2023, 4:20 p.m.