代码主要来自：https://satijalab.org/seurat/articles/integration_introduction.html
1.数据准备
不得不说，网速的限制是无处不在啊。这个数据有点大， 官网给的下载方式是用代码，在大陆基本上不可能成功咯。还是把包下载到本地，用本地安装R包的方法靠谱一点
rm(list = ls())
library(Seurat)
library(SeuratData)
library(patchwork)
# install dataset
#InstallData("ifnb")
#install.packages("ifnb.SeuratData_3.1.0.tar.gz",repos = NULL)
# load dataset
ifnb = LoadData("ifnb")
2.了解和拆分数据
因为是用来做整合的例子，而内置数据是个整体的数据，所以要把它拆分掉。
# split the dataset into a list of two seurat objects (stim and CTRL)
head(ifnb@meta.data)
## orig.ident nCount_RNA nFeature_RNA stim seurat_annotations
## AAACATACATTTCC.1 IMMUNE_CTRL 3017 877 CTRL CD14 Mono
## AAACATACCAGAAA.1 IMMUNE_CTRL 2481 713 CTRL CD14 Mono
## AAACATACCTCGCT.1 IMMUNE_CTRL 3420 850 CTRL CD14 Mono
## AAACATACCTGGTA.1 IMMUNE_CTRL 3156 1109 CTRL pDC
## AAACATACGATGAA.1 IMMUNE_CTRL 1868 634 CTRL CD4 Memory T
## AAACATACGGCATT.1 IMMUNE_CTRL 1581 557 CTRL CD14 Mono
table(ifnb@meta.data$stim)
##
## CTRL STIM
## 6548 7451
ifnb.list <- SplitObject(ifnb, split.by = "stim")
length(ifnb.list)
## [1] 2
可以看到ctrl和stim组各自的细胞数量。
3.完成整合
两个拆分后的对象分别Normalize，找高变化基因，寻找锚点，结合在一起。
# normalize and identify variable features for each dataset independently
ifnb.list <- lapply(X = ifnb.list, FUN = function(x) {
x <- NormalizeData(x)
x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 2000)
})
# select features that are repeatedly variable across datasets for integration
features <- SelectIntegrationFeatures(object.list = ifnb.list)
immune.anchors <- FindIntegrationAnchors(object.list = ifnb.list, anchor.features = features)
# this command creates an 'integrated' data assay
immune.combined <- IntegrateData(anchorset = immune.anchors)
# specify that we will perform downstream analysis on the corrected data note that the
# original unmodified data still resides in the 'RNA' assay
DefaultAssay(immune.combined) <- "integrated"
之后的分析默认使用整合后的数据integrated。
4.常规的降维聚类分群
# Run the standard workflow for visualization and clustering
immune.combined <- ScaleData(immune.combined, verbose = FALSE)
immune.combined <- RunPCA(immune.combined, npcs = 30, verbose = FALSE)
immune.combined <- RunUMAP(immune.combined, reduction = "pca", dims = 1:30)
immune.combined <- FindNeighbors(immune.combined, reduction = "pca", dims = 1:30)
immune.combined <- FindClusters(immune.combined, resolution = 0.5)
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 13999
## Number of edges: 569703
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.9057
## Number of communities: 16
## Elapsed time: 1 seconds
# Visualization
p1 <- DimPlot(immune.combined, reduction = "umap", group.by = "stim")
p2 <- DimPlot(immune.combined, reduction = "umap", label = TRUE, repel = TRUE)
p1 + p2
5.singleR注释
官网使用的是根据marker基因手动识别细胞类型，设置了标签。我这里用singleR偷个懒。。。
singleR分的类比较粗糙，右边那一大片都是单核细胞，没有那么具体。而手动的话可以继续细分。
# 注释
library(celldex)
library(SingleR)
#ref <- celldex::HumanPrimaryCellAtlasData()
ref <- get(load("single_ref/ref_Hematopoietic.RData"))
library(BiocParallel)
pred.scRNA <- SingleR(test = immune.combined@assays$integrated@data,
ref = ref,
labels = ref$label.main,
clusters = immune.combined@active.ident)
pred.scRNA$pruned.labels
## [1] "Monocytes" "CD8+ T cells" "CD4+ T cells" "Monocytes"
## [5] "B cells" "CD8+ T cells" "NK cells" "CD4+ T cells"
## [9] "Monocytes" "B cells" "CD8+ T cells" "Dendritic cells"
## [13] "Monocytes" "Monocytes" "HSCs"
plotScoreHeatmap(pred.scRNA, clusters=pred.scRNA@rownames, fontsize.row = 9,show_colnames = T)
new.cluster.ids <- pred.scRNA$pruned.labels
names(new.cluster.ids) <- levels(immune.combined)
levels(immune.combined)
## [1] "0" "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14"
immune.combined <- RenameIdents(immune.combined,new.cluster.ids)
levels(immune.combined)
## [1] "Monocytes" "CD8+ T cells" "CD4+ T cells" "B cells"
## [5] "NK cells" "Dendritic cells" "HSCs"
UMAPPlot(object = immune.combined, pt.size = 0.5, label = TRUE)
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