plotPairwiseAdjacency.Region

Generate a pairwise adjacency heatmap for a single Region

Usage

plotPairwiseAdjacency.Region(
  object,
  nn,
  feature,
  what = c("log2.enrichment", "p.value", "p.value.enrichment", "p.value.depletion",
    "p.adj", "padj.enrichment", "padj.depletion", "log10.padj", "log10.padj.enrichment",
    "log10.padj.depletion"),
  remove = c("na", "inf", "nan"),
  trim = "all",
  cuts = NULL,
  scaling = "none",
  bottom_pad = 0.2,
  left_pad = 0.2,
  top_pad = 0.2,
  right_pad = 1.5,
  pad_units = "cm",
  aggregate_flag,
  ...
)

Arguments

object: A Region object
nn: The name of a nearestNeighborGraph from object (character).
feature: The name of a cellMetadata column (character).
what: What exactly to plot. The options are given in the default character vector
remove: Character or char vector describing classes to remove, e.g. na, inf, nan
trim: How to trim quantiles - rowwise ("row"), colwise ("col"), or in whole matrix ("all").
cuts: Quantile values to cut. If NULL, trim will not happen.
scaling: Character describing the style of scaling to employ
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.
aggregate_flag: Passed through from higher-level functions to indicate when sample-level aggregation/summarization should be performed. Set to TRUE if pairwiseAdjacency was performed with sample-level aggregation/summarization.
...: Arguments passed to ComplexHeatmap::Heatmap

Usage

Arguments

See also