buildQualityTable: Correct mapping at different tree heights

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

Correct mapping at different tree heights

Description

This function takes as input an ordered set of marker genes (e.g., from at iterative algorithm, and returns an table showing the fraction of cells correctly mapped to a similar cell type (as defined by the heights parameter). A height of 1 indicates correct mapping to the leaf.

Usage

buildQualityTable(
  orderedGenes,
  dend,
  mapDat,
  medianDat,
  clustersF,
  minVal = 2,
  heights = c((0:100)/100),
  verbose = FALSE
)

Arguments

orderedGenes	an ordered list of input genes (e.g. from an iterative algorithm)
dend	dendrogram for mapping.
mapDat	normalized data of the mapping (=reference) data set.
medianDat	median value for each leaf
clustersF	cluster calls for each cell
minVal	minimum number of genes to consider from the list in the mapping
heights	height in the tree to look at
verbose	whether or not to show progress in the function

Value

a matrix of fractions of cells correctly mapped for different tree heights (columns) and different gene panels (rows)

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