incoming_signaling_heatmap: Create a cluster incoming signaling heatmap

In Chris-Cherry/domino: Receptor Ligand Analysis for Single Cell RNA Seq

Create a cluster incoming signaling heatmap

Description

Creates a heatmap of a cluster incoming signaling matrix. Each cluster has a list of ligands capable of activating its enriched transcription factors. The function creates a heatmap of cluster average expression for all of those ligands. A list of all cluster incoming signaling matrices can be found in the cl_signaling_matrices slot of a domino option as an alternative to this plotting function.

Usage

incoming_signaling_heatmap(
  dom,
  rec_clust,
  min_thresh = -Inf,
  max_thresh = Inf,
  scale = "none",
  normalize = "none",
  title = TRUE,
  ...
)

Arguments

dom	A domino object with network built (build_domino)
rec_clust	Which cluster to select as the receptor. Must match naming of clusters in the domino object.
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. 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
title	Either a string to use as the title or a boolean describing whether to include a title. In order to pass the 'main' parameter to NMF::aheatmap you must set title to FALSE.
...	Other parameters to pass to NMF::aheatmap. Note that to use the 'main' parameter of NMF::aheatmap you must set title = FALSE

Chris-Cherry/domino documentation built on Dec. 9, 2024, 12:28 a.m.