seurat5 多样本整合

seurat5 一个参数 五种算法:

Anchor-based RPCA integration (method=RPCAIntegration)
Harmony (method=HarmonyIntegration)
FastMNN (method= FastMNNIntegration)
scVI (method=scVIIntegration)

#CCA
obj <- IntegrateLayers(
  object = obj, method = CCAIntegration,
  orig.reduction = "pca", new.reduction = "integrated.cca",
  verbose = FALSE
)
#RPCA
obj <- IntegrateLayers(
  object = obj, method = RPCAIntegration,
  orig.reduction = "pca", new.reduction = "integrated.rpca",
  verbose = FALSE
)
#Harmony
obj <- IntegrateLayers(
  object = obj, method = HarmonyIntegration,
  orig.reduction = "pca", new.reduction = "harmony",
  verbose = FALSE
)
#FastMNN
obj <- IntegrateLayers(
  object = obj, method = FastMNNIntegration,
  new.reduction = "integrated.mnn",
  verbose = FALSE
)

 NormalizeData(obj) %>%
 FindVariableFeatures()%>%
 ScaleData(features = rownames(.)) %>%  
 RunPCA(features = VariableFeatures(.))  %>%
 IntegrateLayers(HarmonyIntegration)%>%
 FindNeighbors(reduction = 'harmony')%>%
 FindClusters(resolution = 0.5)%>%
 RunUMAP(reduction = "harmony")%>%
 RunTSNE(reduction = "harmony")
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