Create heatmap of cell neighborhoods — neighborhoodHeatmap • SpatialMap

Plots a heatmap of cell neighborhoods

Usage

neighborhoodHeatmap(
  object,
  nn,
  feature,
  col.name = NULL,
  subsample = 0,
  summarize = FALSE,
  summary.fun = "mean",
  scaling = "none",
  cuts = c(0.01, 0.99),
  bottom_pad = 0.2,
  left_pad = 0.2,
  top_pad = 0.2,
  right_pad = 0.2,
  pad_units = "cm",
  ...
)

Arguments

object: A SpatialMap object
nn: A NN graph name
feature: The name of the cellMetadata feature (e.g. cell type) used for defining neighborhoods.
col.name: If a custom col.name was specified when running neighborhoodClusters, you'll need to specify it again here. Default (NULL) is to look for the default value from neighborhoodClusters.
subsample: The heatmap can get very large with large numbers of cells. This is an integer; the matrix will be randomely subsampled to contain this many points.
summarize: Whether to summarize feature counts per neighborhood, rather than explicitly plotting every cell (or, if using subsampling, a subset of cells)
summary.fun: The function used to summarize counts for visualization. Ignored if summarize = FALSE
scaling: Character describing the style of scaling to employ
cuts: Quantile values to cut. If NULL, trim will not happen.
bottom_pad: Padding to add to bottom of plot. Useful if text is getting cut off.
left_pad: Padding to add to left side of plot. Useful if text is getting cut off.
top_pad: Padding to add to top of plot. Useful if text is getting cut off.
right_pad: Padding to add to right side of plot. Useful if text is getting cut off.
pad_units: What units of measurement should the padding values be interpreted as? See ?grid::unit for a list of allowed values.
...: Arguments passed to ComplexHeatmap Heatmap()

Value

A ComplexHeatmap object

Details

See vignette("AnalysisGuide6_Neighborhoods") for a representative workflow that uses this function.