【cellchat】Inference and analysis of cell-cell communication-基础篇，一个condition

最新推荐文章于 2024-09-21 00:18:02 发布

DerekRusso

最新推荐文章于 2024-09-21 00:18:02 发布

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分类专栏：细胞间通讯文章标签： r语言

本文链接：https://blog.csdn.net/DerekRusso/article/details/124264275

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本文介绍了如何使用CellChat工具对细胞间通讯进行推断和分析。内容包括数据预处理、通信网络计算、可视化及系统分析。通过设置不同阈值，可以调整结果的噪音与敏感性。此外，还提供了识别细胞群体在通讯网络中的角色，以及探索信号通路协调性的方法。

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cellchat需要两个输入：基因表达矩阵 + cell label。表达矩阵行为基因列为细胞，标准化+log。cell label为dataframe,行名为细胞，第一列为cell label.

从seurat v3 object中提取cell chat 所需要的两个输入文件：

data.input <- GetAssayData(seurat_object, assay = "RNA", slot = "data") # normalized data matrix
labels <- Idents(seurat_object)
meta <- data.frame(group = labels, row.names = names(labels)) # create a dataframe of the cell labels

library(CellChat)
library(patchwork)
options(stringsAsFactors = FALSE)

part I: data input and preprocessing, initialization of the cellchat object

（1）load data

# Here we load a scRNA-seq data matrix and its associated cell meta data
#load(url("https://ndownloader.figshare.com/files/25950872")) 
# This is a combined data from two biological conditions: normal and diseases

load("/Users/suoqinjin/Documents/CellChat/tutorial/data_humanSkin_CellChat.rda")

data.input = data_humanSkin$data # normalized data matrix

meta = data_humanSkin$meta # a dataframe with rownames containing cell mata data

cell.use = rownames(meta)[meta$condition == "LS"] # extract the cell names from disease data

# Prepare input data for CelChat analysis
data.input = data.input[, cell.use]
meta = meta[cell.use, ]
# meta = data.frame(labels = meta$labels[cell.use], row.names = colnames(data.input)) # manually create a dataframe consisting of the cell labels

unique(meta$labels) # check the cell labels
#>  [1] Inflam. FIB  FBN1+ FIB    APOE+ FIB    COL11A1+ FIB cDC2        
#>  [6] LC           Inflam. DC   cDC1         CD40LG+ TC   Inflam. TC  
#> [11] TC           NKT         
#> 12 Levels: APOE+ FIB FBN1+ FIB COL11A1+ FIB Inflam. FIB cDC1 cDC2 ... NKT

（2）create a cellchat object

cellchat <- createCellChat(object = data.input, meta = meta, group.by = "labels")

（3）set the ligand-receptor interaction database

CellChatDB <- CellChatDB.human # use CellChatDB.mouse if running on mouse data
showDatabaseCategory(CellChatDB)

# Show the structure of the database
dplyr::glimpse(CellChatDB$interaction)

# use a subset of CellChatDB for cell-cell communication analysis
CellChatDB.use <- subsetDB(CellChatDB, search = "Secreted Signaling") # use Secreted Signaling

# use all CellChatDB for cell-cell communication analysis
# CellChatDB.use <- CellChatDB # simply use the default CellChatDB

# set the used database in the object
cellchat@DB <- CellChatDB.use

（4）preprocessing the gene expression data

# subset the expression data of signaling genes for saving computation cost
cellchat <- subsetData(cellchat) # This step is necessary even if using the whole database
future::plan("multiprocess", workers = 4) # do parallel

cellchat <- identifyOverExpressedGenes(cellchat)
cellchat <- identifyOverExpressedInteractions(cellchat)
# project gene expression data onto PPI network (optional)
cellchat <- projectData(cellchat, PPI.human)

Part II: Inference of cell-cell communication network

在核心功能computeCommuProb中，可以设置不同的阈值。默认为trimean(25%),也可以设置成10%、5%等。这个阈值什么意思？当某个cell group中表达某个pair的细胞比例低于此值时，他们的平均表达量就都是零（不会出现在结果里），调低阈值能发现更多通讯，但相应的噪音也更大。调整方法：type = "truncatedMean", trim = 0.1

（1）compute the communication probability and infer the celluar communication network

cellchat <- computeCommunProb(cellchat)

# Filter out the cell-cell communication if there are only few number of cells in certain cell groups
cellchat <- filterCommunication(cellchat, min.cells = 10)

（2） extract the infered celluar communication network as a dataframe