CellChat (version 1.0.0)

rankSimilarity: Rank the similarity of the shared signaling pathways based on their joint manifold learning

Description

Rank the similarity of the shared signaling pathways based on their joint manifold learning

Usage

rankSimilarity(
  object,
  slot.name = "netP",
  type = c("functional", "structural"),
  comparison1 = NULL,
  comparison2 = c(1, 2),
  x.rotation = 90,
  title = NULL,
  color.use = NULL,
  bar.w = NULL,
  font.size = 8
)

Arguments

object

CellChat object

slot.name

the slot name of object that is used to compute centrality measures of signaling networks

type

"functional","structural"

comparison1

a numerical vector giving the datasets for comparison. This should be the same as `comparison` in `computeNetSimilarityPairwise`

comparison2

a numerical vector with two elements giving the datasets for comparison.

If there are more than 2 datasets defined in `comparison1`, `comparison2` can be defined to indicate which two datasets used for computing the distance. e.g., comparison2 = c(1,3) indicates the first and third datasets defined in `comparison1` will be used for comparison.

x.rotation

rotation of x-labels

title

main title of the plot

color.use

defining the color

bar.w

the width of bar plot

font.size

font size

Value