buildTreeFromGenePanel: Build and plot dendrogram from gene panel

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

Build and plot dendrogram from gene panel

Description

Build and plot a dendrogram using correlation-based average linkage hierarchical clustering and only using a specified set of genes. The output is the expected accuracy of mapping to each node in the tree, which gives an idea of the best-case expected results for mFISH analysis.

Usage

buildTreeFromGenePanel(
  dend = NA,
  refDat = NA,
  mapDat = refDat,
  medianDat = NA,
  requiredGenes = 2,
  clusters = NA,
  mappedAsReference = FALSE,
  genesToMap = rownames(mapDat),
  plotdendro = TRUE,
  returndendro = TRUE,
  mar = c(12, 5, 5, 5),
  main = NULL,
  ylab = NULL,
  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
requiredGenes	minimum number of genes required to be expressed in a cluster (column of medianDat) for the cluster to be included (default=2)
clusters	cluster calls for each cell
mappedAsReference	if TRUE, returns the fraction of cells mapped to a node which are were orginally clustered from that node; if FALSE (default) returns the fraction of cells clustered under a node which are mapped to the correct node.
genesToMap	which genes to include in the correlation mapping
plotdendro	should the dendrogram be plotted (default = TRUE)
mar	margins (for use with par)
main, ylab	add title and labels to plot (default is NULL)
use, ...	additional parameters for cor
returnDendro	should the dendrogram be returned (default = TRUE)

Value

a list where the first entry is the resulting tree and the second entry is the fraction of cells correctly mapping to each node using the inputted gene panel.

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