corTreeMapping: Correlation-based cluster mapping

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

Correlation-based cluster mapping

Description

Primary function for doing correlation-based mapping to cluster medians. This is wrapper for cor and returns a correlation matrix.

Usage

corTreeMapping(
  mapDat,
  medianDat,
  dend = NULL,
  refDat = NA,
  clusters = NA,
  genesToMap = rownames(mapDat),
  use = "p",
  method = "p"
)

Arguments

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
dend	dendrogram for mapping. If provided, correlations to nodes are also returned
refDat	normalized data of the REFERENCE data set. Ignored if medianDat is passed
clusters	cluster calls for each cell. Ignored if medianDat is passed
genesToMap	which genes to include in the correlation mapping
use	additional parameter for cor (use='p' as default)
method	additional parameter for cor (method='p' as default)

Value

matrix with the correlation between expression of each cell and representative value for each leaf and node

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