plotLR: plot one specific ligand-receptor pair

In liuqivandy/SpaGene: Identify spatially localized genes and colocalized gene pairs

plot one specific ligand-receptor pair

Description

plot one specific ligand-receptor pair to find the colocalized region

Usage

plotLR(
  expr,
  location,
  normalize = T,
  topn = floor(0.2 * dim(location)[1]),
  knn = 8,
  LRpair = c("Ptn", "Ptprz1"),
  pt.size = 2,
  alpha.min = 0.1,
  max.cut = 0.95
)

Arguments

expr	gene expression matrix, the row is the gene and the column is the spot/cell
location	location matrix, the row number of location should match the column number of expr
normalize	whether to normalize the data (default: TRUE)
topn	the number of spots/cells considered high expression (default: 20 percent of the total spots/cells)
knn	the number of nearest neighbours to search (default: 8)
LRpair	the ligand-receptor pair for plot
pt.size	the point size (default:2)
alpha.min	the alpha for the minimum value (default:0.1)
max.cut	the maximum cutoff for the LR activity

Value

a data frame containing the result of each ligand-receptor pair

liuqivandy/SpaGene documentation built on July 1, 2023, 6:44 a.m.