Create a network heatmap — signaling

Creates a heatmap of the signaling network. Alternatively, the network matrix can be accessed directly in the signaling slot of a domino object.

Usage

signaling_heatmap(
  dom,
  clusts = NULL,
  min_thresh = -Inf,
  max_thresh = Inf,
  scale = "none",
  normalize = "none",
  ...
)

Arguments

dom: Domino object with network built (build_domino())
clusts: Vector of clusters to be included. If NULL then all clusters are used.
min_thresh: Minimum signaling threshold for plotting. Defaults to -Inf for no threshold.
max_thresh: Maximum signaling threshold for plotting. Defaults to Inf for no threshold.
scale: How to scale the values (after thresholding). Options are 'none', 'sqrt' for square root, or 'log' for log10.
normalize: Options to normalize the matrix. Normalization is done after thresholding and scaling. Accepted inputs are 'none' for no normalization, 'rec_norm' to normalize to the maximum value with each receptor cluster, or 'lig_norm' to normalize to the maximum value within each ligand cluster
...: Other parameters to pass to ComplexHeatmap::Heatmap()

Value

a Heatmap rendered to the active graphics device

Examples

#basic usage
signaling_heatmap(dominoSignal:::pbmc_dom_built_tiny)

#scale
signaling_heatmap(dominoSignal:::pbmc_dom_built_tiny, scale = "sqrt")

#normalize
signaling_heatmap(dominoSignal:::pbmc_dom_built_tiny, normalize = "rec_norm")
#> Warning: Some values are NA, replacing with 0s.