Plot expression of a receptor's ligands by other cell types as a chord plot

Creates a chord plot of expression of ligands that can activate a specified receptor where chord widths correspond to mean ligand expression by the cluster.

Usage

circos_ligand_receptor(
  dom,
  receptor,
  ligand_expression_threshold = 0.01,
  cell_idents = NULL,
  cell_colors = NULL
)

Arguments

dom

Domino object that has undergone network building with build_domino()

receptor

Name of a receptor active in at least one cell type in the domino object

ligand_expression_threshold

Minimum mean expression value of a ligand by a cell type for a chord to be rendered between the cell type and the receptor

cell_idents

Vector of cell types from cluster assignments in the domino object to be included in the plot.

cell_colors

Named vector of color names or hex codes where names correspond to the plotted cell types and the color values

Value

renders a circos plot to the active graphics device

Examples

#basic usage
circos_ligand_receptor(dominoSignal:::pbmc_dom_built_tiny, receptor = "CXCR3")
#> There are more than one numeric columns in the data frame. Take the
#> first two numeric columns and draw the link ends with unequal width.
#> 
#> Type `circos.par$message = FALSE` to suppress the message.

#specify colors
cols = c("red", "orange", "green", "blue", "pink", "purple", "slategrey", "firebrick", "hotpink")
names(cols) = levels(dom_clusters(dominoSignal:::pbmc_dom_built_tiny))
circos_ligand_receptor(dominoSignal:::pbmc_dom_built_tiny, receptor = "CXCR3", cell_colors = cols)
#> There are more than one numeric columns in the data frame. Take the
#> first two numeric columns and draw the link ends with unequal width.
#> 
#> Type `circos.par$message = FALSE` to suppress the message.