单细胞聚类方法

Partitioning-based clustering

kmeans：K均值
论文链接

res <- kmeans(t(data), centers = 9)
adjustedRandIndex(res$cluster, meta$label)
plot(res$centers, col = topo.colors(4))

tsne_out <- Rtsne(data)
plot(tsne_out$Y, col = topo.colors(4))

SAIC：在聚类迭代过程中结合k-means和ANOVA

SCUBA：kmeans；使用gap statistics 识别bifurcation events

scVDMC : single-cell variance-driven multi-task clustering

pcaReduce：
论文链接

library(pcaReduce)
res <- PCAreduce(t(data),
                 nbt = 1,
                 q = 7,
                 method = "S")
res[[1]]
adjustedRandIndex(res[[1]][, 1], meta$label)

k-medoids

res <- pamk(data = t(data), krange = 7)
adjustedRandIndex(res$pamobject$clustering, meta$label)

层次聚类

BackSPIN：two-way biclustering algorithm；

cellTree：构建最小生成树；

CIDR：缺失值填补
论文链接

#rows correspond to features (genes, transcripts, etc) and the columns correspond to cells
library(cidr)
load("/Biase.Rdata")

cellType <- factor(meta$label)
types <- levels(cellType)

scols <-
  c("red",
    "blue"