Create a custom heatmap of copy number data

This function takes a scCNVisObject and outputs a ComplexHeatmap::Heatmap object

makeSCHeatmap(
  obj,
  gr = NULL,
  annotations = NULL,
  annotation.colors = NULL,
  group = NULL,
  secondary.group = NULL,
  show.annotation.name = FALSE,
  add.noise = T,
  border = FALSE,
  post.plot.mod.fun = NULL,
  heatmap.colors = NULL,
  legend.title = "Value",
  plot.title = NULL,
  verbose = F
)

Arguments

obj

A scCNVisObject made using createPlotObject()

gr

A GenomicRanges:GRanges object of the regions to graph. If NULL, all regions will be plotted. Default = NULL

annotations

Column names from obj metadata to use for annotating cells on the left of the plot. Default = NULL

annotation.colors

Colors used in annotation. See heatmap vignette for example. Default = NULL

group

Name of metadata column. Signal will be averaged across all cells in each group. Default = NULL

secondary.group

Name of metadata column. Can be used to add a secondary annotation describing the composition of 'group'. Default = NULL

show.annotation.name

Show annotation names. Does nothing if annotations is NULL. Default == NULL

add.noise

Add minor noise to the data for clustering purposes. The visualization will not include the noise. Default = TRUE

border

Draw borders. Default = FALSE

post.plot.mod.fun

A function to apply to plot data before final plotting. Default == NULL

heatmap.colors

Named vector of numeric values. Names should be colors, values correspond to values in the heatmap. If NULL, a red/white/blue color ramp will be used, centered on the median. Default = NULL

legend.title

Title for the legend describing the heatmap. Often something like "log2(copy ratio)" or some other metric. Default = "Value"

plot.title

Plot title

verbose

Verbose logging. Default = FALSE

Value

Returns a list containing a "Plot" (ComplexHeatmap) and "PlotData" (matrix)