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")
