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,
clusts = NULL,
min_thresh = -Inf,
max_thresh = Inf,
scale = "none",
normalize = "none",
title = TRUE,
...
)Arguments
- dom
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.
- 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. 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
ComplexHeatmap::Heatmap()you must set title to FALSE.- ...
Other parameters to pass to
ComplexHeatmap::Heatmap(). Note that to use the 'column_title' parameter ofComplexHeatmap::Heatmap()you must set title = FALSE
Examples
example(build_domino, echo = FALSE)
#incoming signaling of the CD8 T cells
incoming_signaling_heatmap(pbmc_dom_built_tiny, "CD8_T_cell")
