visualize\(data\)similarity

visualize pre-computed similarity matrices

Description

Internal helper for similarity heatmaps. Set context = “obs” to work on data$obsp matrices (observation similarity) and context = “mod” to work on data$modp matrices (model similarity). Requires installed packages .pkg ComplexHeatmap and .pkg circlize.

Usage

.visualize.similarity(
  data,
  key,
  type = "heatmap",
  cluster = TRUE,
  label.by = NULL,
  cols = colorRampPalette(c("darkgreen", "white", "darkorchid4")),
  n.breaks = 11L,
  symmetrize.range = FALSE,
  center.zero = FALSE,
  drop.na = TRUE,
  context = c("obs", "mod"),
  ...
)

Arguments

data	A PolyGeniusData object.
key	Name of the similarity matrix stored in data$obsp or data$modp.
type	Plot type. Currently only “heatmap” is supported.
cluster	Logical; whether to cluster rows and columns.
label.by	Optional column name from data$obs or data$mod for labels.
cols	A colorRampPalette function used to generate colors.
n.breaks	Integer number of color breaks sampled from cols.
symmetrize.range	Logical; if TRUE, use a symmetric range around zero.
center.zero	Logical; if TRUE, center the color scale at zero.
drop.na	Logical; drop rows/columns that are entirely NA.
context	Character; “obs” for obsp, “mod” for modp.
…	Additional arguments passed to ComplexHeatmap::Heatmap().