CellChat-class: The key slots used in the CellChat object are described...

In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

The key slots used in the CellChat object are described below.

Description

The key slots used in the CellChat object are described below.

Slots

data.raw

raw count data matrix

data

normalized data matrix for CellChat analysis (Genes should be in rows and cells in columns)

data.signaling

a subset of normalized matrix only containing signaling genes

data.scale

scaled data matrix

data.project

projected data

images

a list of spatial image objects

net

a three-dimensional array P (K×K×N), where K is the number of cell groups and N is the number of ligand-receptor pairs. Each row of P indicates the communication probability originating from the sender cell group to other cell groups.

netP

a three-dimensional array representing cel-cell communication networks on a signaling pathway level

DB

ligand-receptor interaction database used in the analysis (a subset of CellChatDB)

LR

a list of information related with ligand-receptor pairs

meta

data frame storing the information associated with each cell

idents

a factor defining the cell identity used for all analysis. It becomes a list for a merged CellChat object

var.features

A list: one element is a vector consisting of the identified over-expressed signaling genes; one element is a data frame returned from the differential expression analysis

dr

List of the reduced 2D coordinates, one per method, e.g., umap/tsne/dm

options

List of miscellaneous data, such as parameters used throughout analysis, and a indicator whether the CellChat object is a single or merged

sqjin/CellChat documentation built on Nov. 10, 2023, 4:29 a.m.