Monocle3

Monocle3的安装

• 见博客https://www.jianshu.com/p/78eeae93c5a0

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Monocle3示例代码

• 将Seurat对象转为cds对象

Seurat2Monocle3 <- function(Seurat_Object){
  library(monocle3)
  library(Seurat)
  data <- as(as.matrix(Seurat_Object@assays$RNA@counts), 'sparseMatrix')
  pd <-  tumor@meta.data
  fd <- data.frame(gene_short_name = row.names(data), row.names = row.names(data))     # 基因注释必须包含一列名为“gene_short_name” 
  cds <- new_cell_data_set(data,
                           cell_metadata  = pd,
                           gene_metadata  = fd)
  return(cds)
}
tumor <- readRDS('../data8/tumor4_0830.RDS')
tumor_cds <- Seurat2Monocle3(tumor)

• 创建cds对象

tumor_cds <- Seurat2Monocle3(tumor)

• PCA降维

tumor_cds <- preprocess_cds(tumor_cds, num_dim = 100)
plot_pc_variance_explained(tumor_cds)

• UMAP可视化

tumor_cds <- reduce_dimension(tumor_cds, preprocess_method = 'PCA')
plot_cells(tumor_cds, color_cells_by="batch")

• MNN去批次效应

tumor_cds = align_cds(tumor_cds, alignment_group = "batch",alignment_k = 20)
tumor_cds = reduce_dimension(tumor_cds)
plot_cells(tumor_cds, color_cells_by="batch", label_cell_groups=FALSE)
plot_cells(tumor_cds, color_cells_by="scref17.MK")
plot_cells(tumor_cds, genes=c("GFAP","EGFR",'TOP2A','CDK1'))

• 聚类细胞

tumor_cds <- cluster_cells(tumor_cds)
plot_cells(tumor_cds, color_cells_by = "partition")

• 学习轨迹

tumor_cds <- learn_graph(tumor_cds)
plot_cells(tumor_cds,color_cells_by = "scref17.MK", cell_size = 0.5,label_cell_groups=FALSE)

• 排序细胞

# 手动鼠标选择起点
tumor_cds <- order_cells(tumor_cds)
# 手动指定选择起点
tumor_cds <- order_cells(tumor_cds, root_pr_nodes=c('Y_4','Y_8'))
plot_cells(tumor_cds,color_cells_by = "pseudotime")

• 3d轨迹图

cds_3d <- reduce_dimension(tumor_cds, max_components = 3)
cds_3d <- cluster_cells(cds_3d)
cds_3d <- learn_graph(cds_3d)
plot_cells_3d(cds_3d, color_cells_by="scref17.MK")
cds_3d <- order_cells(cds_3d)
plot_cells_3d(cds_3d, color_cells_by="scref17.MK")

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参考

Blog: https://www.jianshu.com/p/e94cff521ebc
Tutorial：https://cole-trapnell-lab.github.io/monocle3/
Paper：https://www.nature.com/articles/s41586-019-0969-x

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