View source: R/heatmapGenerators.R
makeMetaclusterHeatmaps | R Documentation |
Generate heatmaps from a metaclustered experiment
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
)
experiment |
A discovrExperiment created using |
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 |
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 |
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 |
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 |
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) |
An S3 object of class discovrExperiment
Mario G Rosasco, Virginia Muir
setupDiscovrExperiment
clusterDiscovrExperiment
metaclusterDiscovrExperiment
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