makeDensityHeatmap: Make annotated heatmap of cell type densities

In caitlinjones/halo: Development version of the package 'halo', which analyzes and visualizes Halo data

Description

Make annotated heatmap of cell type densities

Usage

makeDensityHeatmap(den, annot = NULL, annotColors = NULL,
  msToSummarize = NULL, ctConfig = NULL, areas = NULL,
  separateLegend = FALSE, bySample = TRUE, byFOV = TRUE,
  clusterFOVs = TRUE, clusterSamples = TRUE)

Arguments

den	table containing total FOV cell type densities with basic FOV/Sample annotations
annot	table of additional FOV annotation to include in annot tracks
annotColors	list of annotation legend colors, where keys match column names in annot, and each value is a vector of colors named by the respective annotation values
msToSummarize	a vector of marker set names to collapse into one "cell type"; if given, must provide a parsed cell type configuration and FOV area table; any mutually-exclusive (stackable) cell types belonging to a marker set in this vector will be converted to a single density value for each FOV.
ctConfig	if summarizing any marker sets, must provide a cell type config returned by getMarkerConfig()
areas	if summarizing any marker sets, must provide table of FOV areas in order to calculate new density.

caitlinjones/halo documentation built on May 7, 2019, 8 a.m.