makeMetaclusterHeatmaps: Generate heatmaps from a metaclustered experiment

In BenaroyaResearch/briDiscovr: Distribution analysis across clusters of a parent population overlaid with a rare subpopulation

Generate heatmaps from a metaclustered experiment

Description

Generate heatmaps from a metaclustered experiment

Usage

makeMetaclusterHeatmaps(
  experiment,
  childSubsets = NA,
  dropMarkers = NA,
  filenamePrefix = NA,
  parentTitle = "Parent",
  metaclusterColors = NA,
  zScoreBreaks = c(-2, 0, 2),
  zScoreColors = c("#00FFFF", "#000000", "#FDE725"),
  intensityBreaks = c(0, 2, 4, 6),
  intensityColors = c("#4A0E53", "#925F54", "#D6B343", "#FDE727"),
  columnDendHeight = 10,
  rowDendWidth = 10,
  verbose = TRUE
)

Arguments

experiment	A discovrExperiment created using setupDiscovrExperiment, clustered using clusterDiscovrExperiment, and metaclustered with metaclusterDiscovrExperiment
childSubsets	A vector of strings indicating which subsets represent rare populations (eg: Tmr+ cells). If this is left NA, then it's assumed all non-parent subsets are rare populations. (default: NA)
dropMarkers	A string or vector of strings indicating names of markers to exclude from display. Note that printing the experiment object will display a list of all markers. By default all markers will be included. Markers not used in metaclustering will be shown in a separate heatmap. Also note that you cannot drop markers that were used in metaclustering, and should instead re-run the metclustering step, dropping the markers at that stage. (default: NA)
filenamePrefix	A string indicating the prefix to use for each file that gets saved. This can include a directory path. If left as NA, will use the current date as the prefix with the format YYMMDD. (default: NA)
parentTitle	A string to use to label the parent population heatmaps (default: "Parent")
metaclusterColors	An optional vector of color values to use to label metaclusters in heatmaps. If left as the default 'NA', a random list of visually distinct colors will be generated. Note that if a color vector is supplied, it must contain at least as many colors as there are metaclusters. (default: NA)
zScoreBreaks	A vector of numbers indicating the values used to calibrate the Z score color scale. This vector must have the same number of values as zScoreColors. (default: c(-2,0,2))
zScoreColors	A vector of strings indicating the colors used to represent the Z score value range. This vector must have the same number of values as zScoreBreaks. (default: c("#00FFFF", "#000000", "#FDE725"))
intensityBreaks	A vector of numbers indicating the values used to calibrate the transformed marker intensity scale. This vector must have the same number of values as intensityColors (default: c(0,2,4,6))
intensityColors	A vector of strings indicating the colors used to represent the transformed marker intensity value range. This vector must have the same number of values as intensityBreaks (default: c("#4A0E53", "#925F54", "#D6B343", "#FDE727"))
columnDendHeight	A numeric indicating the column dendrogram height (in mm) for the Z score cluster phenotypes heatmap (default: 10)
rowDendWidth	A numeric indicating the row dendrogram width (in mm) for the Z score cluster phenotypes heatmap (default: 10)
verbose	A boolean specifying whether to display processing messages (default: TRUE)

Value

An S3 object of class discovrExperiment

Author(s)

Mario G Rosasco, Virginia Muir

See Also

setupDiscovrExperiment clusterDiscovrExperiment metaclusterDiscovrExperiment

BenaroyaResearch/briDiscovr documentation built on March 15, 2024, 12:31 a.m.