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gse123902_monocle3.R
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#if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#BiocManager::install(version = '3.17')
#BiocManager::install("Cairo",force = TRUE)
setwd("~/gse123902/CytoTRACE")
library(Seurat)
library(monocle3)
library(tidyverse)
library(patchwork)
library(Cairo)
#https://cole-trapnell-lab.github.io/monocle3/docs/installation/
#library(monocle)#can not use this package.error will come out.
seurat <- readRDS(file="n4_cluster_id.rds")
DimPlot(seurat, label = T) + NoLegend()
DimPlot(seurat, label = T)
table(Idents(seurat))
##创建CDS对象并预处理数据
data <- GetAssayData(seurat, assay = 'RNA', slot = 'counts')
cell_metadata <- [email protected]
gene_annotation <- data.frame(gene_short_name = rownames(data))
rownames(gene_annotation) <- rownames(data)
cds <- new_cell_data_set(data,
cell_metadata = cell_metadata,
gene_metadata = gene_annotation)
#preprocess_cds函数相当于seurat中NormalizeData+ScaleData+RunPCA
cds <- preprocess_cds(cds, num_dim = 50)
plot_pc_variance_explained(cds)#pca analysis
#umap,tSNE降维
cds <- reduce_dimension(cds, preprocess_method = "PCA")
plot_cells(cds)
colnames(colData(cds))
p1 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="tech") + ggtitle('cds.umap')
p1
p2 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="celltype") + ggtitle('cds.umap')
p2
cds <- reduce_dimension(cds, reduction_method = "tSNE")
p3 <- plot_cells(cds, reduction_method="tSNE", color_cells_by="tech")
p3
p4 <- plot_cells(cds, reduction_method="tSNE", color_cells_by="celltype")
p4
##从seurat导入整合过的umap坐标
cds.embed <- cds@int_colData$reducedDims$UMAP
int.embed <- Embeddings(seurat, reduction = "umap")
int.embed <- int.embed[rownames(cds.embed),]
cds@int_colData$reducedDims$UMAP <- int.embed
p2 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="celltype") + ggtitle('int.umap')
p1|p2
p3 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="tech") + ggtitle('int.umap')
p3
## Monocle3聚类分区
cds <- cluster_cells(cds,cluster_method='louvain')#bug only work with cluster_method='louvain'
p1 <- plot_cells(cds, show_trajectory_graph = FALSE) + ggtitle("label by clusterID")
p2 <- plot_cells(cds, color_cells_by = "partition", show_trajectory_graph = FALSE) +
ggtitle("label by partitionID")
p = wrap_plots(p1, p2)
p
colData(cds)$assigned_cell_type <- as.character(partitions(cds))
colData(cds)$assigned_cell_type <- dplyr::recode(colData(cds)$seurat_clusters,
"0"="Thelper", "1"="Cytotoxic_cd8","2"="Naive_cd4","3"="Cytotoxic_cd8","4"="Macrophage","5"="Macrophage",
"6"="Cytotoxic_cd8","7"="Progenitor_cd8 ","8"="Monocyte","9"="Monocyte","10"="Macrophage","11"="Macrophage",
"12"="Cytotoxic_cd8","13"="Cytotoxic_cd8","14"="Macrophage","15"="Epithelial","16"="Effector_memory_cd8",
"17"="Epithelial","18"="Mast","19"="Progenitor","20"="Epithelial","21"="B","22"="Chronic_activation_cd4",
"23"="Macrophage","24"="Epithelial","25"="B","26"="Macrophage")
colnames(colData(cds))
cds <- learn_graph(cds)
p1= plot_cells(cds, label_groups_by_cluster = FALSE, label_leaves = FALSE,
label_branch_points = FALSE)
p1
p2 = plot_cells(cds,color_cells_by = "celltype",label_groups_by_cluster = FALSE,label_cell_groups = FALSE,
label_leaves = TRUE, label_branch_points = TRUE,graph_label_size = 8)
p2
p3 = plot_cells(cds,color_cells_by = "tech",label_groups_by_cluster = FALSE,label_cell_groups = FALSE,
label_leaves = TRUE, label_branch_points = TRUE,graph_label_size = 8)
p3
p5 = plot_cells(cds,color_cells_by = "assigned_cell_type",label_cell_groups = FALSE, label_groups_by_cluster = TRUE,
label_leaves = TRUE, label_branch_points = TRUE,graph_label_size = 5)
p5
#细胞按拟时排序
cds <- order_cells(cds) #dragging a rectangle,then choose,done
#plot_cells(cds, color_cells_by = "pseudotime", label_cell_groups = FALSE,
# label_leaves = FALSE, label_branch_points = FALSE,graph_label_size = 4)
#p + geom_vline(xintercept = seq(-5,-4,0.25)) + geom_hline(yintercept = seq(3,4,0.25))
#embed <- data.frame(Embeddings(seurat, reduction = "umap"))
#embed <- subset(embed, UMAP_1 > -5 & UMAP_1 < -4.75 & UMAP_2 > 3& UMAP_2 < 3.25)
#root.cell <- rownames(embed)
#cds <- order_cells(cds, root_cells = root.cell)
#plot_cells(cds, color_cells_by = "pseudotime", label_cell_groups = FALSE,
# label_leaves = FALSE, label_branch_points = FALSE, graph_label_size = 4)
##寻找拟时轨迹差异基因,graph_test分析最重要的结果是莫兰指数（morans_I），其值在-1至1之间，0代表此基因没有
#空间共表达效应，1代表此基因在空间距离相近的细胞中表达值高度相似。#long time
#Track_genes <- graph_test(cds, neighbor_graph="principal_graph", cores=10)#take long time
#Track_genes<-read.csv("Trajectory_genes.csv", sep=",",row.names = 1)
#write.csv(Track_genes,"Trajectory_genes01.csv",row.names = TRUE)
#13 genes morans_I>0.6 compared with 166_immune_gene
Track<-c("FTL","IFNG","CCL5","CD27","TIGIT","CTLA4","TNFRSF9","CCR1","TNFRSF4")
plot_genes_in_pseudotime(cds[Track,], color_cells_by="assigned_cell_type", min_expr=0.5, ncol = 3)
#FeaturePlot图
#plot_cells(cds, genes=Track, show_trajectory_graph=FALSE,label_cell_groups=FALSE, label_leaves=FALSE)
seurat <- readRDS(file="p8_cluster_id.rds")
DimPlot(seurat, label = T) + NoLegend()
DimPlot(seurat, label = T)
table(Idents(seurat))
##创建CDS对象并预处理数据
data <- GetAssayData(seurat, assay = 'RNA', slot = 'counts')
cell_metadata <- [email protected]
gene_annotation <- data.frame(gene_short_name = rownames(data))
rownames(gene_annotation) <- rownames(data)
cds <- new_cell_data_set(data,
cell_metadata = cell_metadata,
gene_metadata = gene_annotation)
#preprocess_cds函数相当于seurat中NormalizeData+ScaleData+RunPCA
cds <- preprocess_cds(cds, num_dim = 50)
plot_pc_variance_explained(cds)#pca analysis
#umap,tSNE降维
cds <- reduce_dimension(cds, preprocess_method = "PCA")
plot_cells(cds)
colnames(colData(cds))
p1 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="tech") + ggtitle('cds.umap')
p1
p2 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="celltype") + ggtitle('cds.umap')
p2
cds <- reduce_dimension(cds, reduction_method = "tSNE")
p3 <- plot_cells(cds, reduction_method="tSNE", color_cells_by="tech")
p3
p4 <- plot_cells(cds, reduction_method="tSNE", color_cells_by="celltype")
p4
##从seurat导入整合过的umap坐标
cds.embed <- cds@int_colData$reducedDims$UMAP
int.embed <- Embeddings(seurat, reduction = "umap")
int.embed <- int.embed[rownames(cds.embed),]
cds@int_colData$reducedDims$UMAP <- int.embed
p2 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="celltype") + ggtitle('int.umap')
p1|p2
p3 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="tech") + ggtitle('int.umap')
p3
## Monocle3聚类分区
cds <- cluster_cells(cds,cluster_method='louvain')#bug only work with cluster_method='louvain'
p1 <- plot_cells(cds, show_trajectory_graph = FALSE) + ggtitle("label by clusterID")
p2 <- plot_cells(cds, color_cells_by = "partition", show_trajectory_graph = FALSE) +
ggtitle("label by partitionID")
p = wrap_plots(p1, p2)
p
colData(cds)$assigned_cell_type <- as.character(partitions(cds))
colData(cds)$assigned_cell_type <- dplyr::recode(colData(cds)$seurat_clusters,
"0"="Effector_cd4","1"="B","2"="nkt","3"="Effector_cd8","4"="Effector_cd8","5"="Effector_cd8","6"="macrophage",
"7"="Thelper","8"="Thelper","9"="nk","10"="Thelper","11"="B","12"="progenitor","13"="epithelial","14"="nk",
"15"="mast","16"="macrophage","17"="macrophage","18"="progenitor","19"="epithelial","20"="endothelial",
"21"="B","22"="B","23"="B","24"="progenitor","25"="B","26"="Pre_exhasted_cd8" )
colnames(colData(cds))
cds <- learn_graph(cds)
p1= plot_cells(cds, label_groups_by_cluster = FALSE, label_leaves = FALSE,
label_branch_points = FALSE)
p1
p2 = plot_cells(cds,color_cells_by = "celltype",label_groups_by_cluster = FALSE,label_cell_groups = FALSE,
label_leaves = TRUE, label_branch_points = TRUE,graph_label_size = 8)
p2
p3 = plot_cells(cds,color_cells_by = "tech",label_groups_by_cluster = FALSE,label_cell_groups = FALSE,
label_leaves = TRUE, label_branch_points = TRUE,graph_label_size = 8)
p3
p5 = plot_cells(cds,color_cells_by = "assigned_cell_type",label_cell_groups = FALSE, label_groups_by_cluster = TRUE,
label_leaves = TRUE, label_branch_points = TRUE,graph_label_size = 5)
p5
#细胞按拟时排序
cds <- order_cells(cds) #dragging a rectangle,then choose,done
#plot_cells(cds, color_cells_by = "pseudotime", label_cell_groups = FALSE,
# label_leaves = FALSE, label_branch_points = FALSE,graph_label_size = 4)
#p + geom_vline(xintercept = seq(-5,-4,0.25)) + geom_hline(yintercept = seq(3,4,0.25))
#embed <- data.frame(Embeddings(seurat, reduction = "umap"))
#embed <- subset(embed, UMAP_1 > -5 & UMAP_1 < -4.75 & UMAP_2 > 3& UMAP_2 < 3.25)
#root.cell <- rownames(embed)
#cds <- order_cells(cds, root_cells = root.cell)
#plot_cells(cds, color_cells_by = "pseudotime", label_cell_groups = FALSE,
# label_leaves = FALSE, label_branch_points = FALSE, graph_label_size = 4)
##寻找拟时轨迹差异基因,graph_test分析最重要的结果是莫兰指数（morans_I），其值在-1至1之间，0代表此基因没有
#空间共表达效应，1代表此基因在空间距离相近的细胞中表达值高度相似。#long time
#Track_genes <- graph_test(cds, neighbor_graph="principal_graph", cores=10)#take long time
#Track_genes<-read.csv("Trajectory_genes.csv", sep=",",row.names = 1)
#write.csv(Track_genes,"Trajectory_genes01.csv",row.names = TRUE)
#13 genes morans_I>0.6 compared with 166_immune_gene
Track<-c("FTL","IFNG","CCL5","CD27","TIGIT","CTLA4","TNFRSF9","CCR1","TNFRSF4")
plot_genes_in_pseudotime(cds[Track,], color_cells_by="assigned_cell_type", min_expr=0.5, ncol = 3)
#FeaturePlot图
#plot_cells(cds, genes=Track, show_trajectory_graph=FALSE,label_cell_groups=FALSE, label_leaves=FALSE)
seurat <- readRDS(file="m5_cluster_id.rds")
DimPlot(seurat, label = T) + NoLegend()
DimPlot(seurat, label = T)
table(Idents(seurat))
##创建CDS对象并预处理数据
data <- GetAssayData(seurat, assay = 'RNA', slot = 'counts')
cell_metadata <- [email protected]
gene_annotation <- data.frame(gene_short_name = rownames(data))
rownames(gene_annotation) <- rownames(data)
cds <- new_cell_data_set(data,
cell_metadata = cell_metadata,
gene_metadata = gene_annotation)
#preprocess_cds函数相当于seurat中NormalizeData+ScaleData+RunPCA
cds <- preprocess_cds(cds, num_dim = 50)
plot_pc_variance_explained(cds)#pca analysis
#umap,tSNE降维
cds <- reduce_dimension(cds, preprocess_method = "PCA")
plot_cells(cds)
colnames(colData(cds))
p1 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="tech") + ggtitle('cds.umap')
p1
p2 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="celltype") + ggtitle('cds.umap')
p2
cds <- reduce_dimension(cds, reduction_method = "tSNE")
p3 <- plot_cells(cds, reduction_method="tSNE", color_cells_by="tech")
p3
p4 <- plot_cells(cds, reduction_method="tSNE", color_cells_by="celltype")
p4
##从seurat导入整合过的umap坐标
cds.embed <- cds@int_colData$reducedDims$UMAP
int.embed <- Embeddings(seurat, reduction = "umap")
int.embed <- int.embed[rownames(cds.embed),]
cds@int_colData$reducedDims$UMAP <- int.embed
p2 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="celltype") + ggtitle('int.umap')
p1|p2
p3 <- plot_cells(cds, reduction_method="UMAP", color_cells_by="tech") + ggtitle('int.umap')
p3
## Monocle3聚类分区
cds <- cluster_cells(cds,cluster_method='louvain')#bug only work with cluster_method='louvain'
p1 <- plot_cells(cds, show_trajectory_graph = FALSE) + ggtitle("label by clusterID")
p2 <- plot_cells(cds, color_cells_by = "partition", show_trajectory_graph = FALSE) +
ggtitle("label by partitionID")
p = wrap_plots(p1, p2)
p
colData(cds)$assigned_cell_type <- as.character(partitions(cds))
colData(cds)$assigned_cell_type <- dplyr::recode(colData(cds)$seurat_clusters,
"0"="cytotoxic_cd8","1"="Recently_activated_cd4","2"="cytotoxic_cd8",
"3"="epithelial", "4"="Effector_memory_cd4","5"="macrophage","6"="Treg",
"7"="epithelial", "8"="neutrophil","9"="B","10"="macrophage","11"="B",
"12"="macrophage","13"="macrophage", "14"="progenitor" )
colnames(colData(cds))
cds <- learn_graph(cds)
p1= plot_cells(cds, label_groups_by_cluster = FALSE, label_leaves = FALSE,
label_branch_points = FALSE)
p1
p2 = plot_cells(cds,color_cells_by = "celltype",label_groups_by_cluster = FALSE,label_cell_groups = FALSE,
label_leaves = TRUE, label_branch_points = TRUE,graph_label_size = 8)
p2
p3 = plot_cells(cds,color_cells_by = "tech",label_groups_by_cluster = FALSE,label_cell_groups = FALSE,
label_leaves = TRUE, label_branch_points = TRUE,graph_label_size = 8)
p3
p5 = plot_cells(cds,color_cells_by = "assigned_cell_type",label_cell_groups = FALSE, label_groups_by_cluster = TRUE,
label_leaves = TRUE, label_branch_points = TRUE,graph_label_size = 5)
p5
#细胞按拟时排序
cds <- order_cells(cds) #dragging a rectangle,then choose,done
#plot_cells(cds, color_cells_by = "pseudotime", label_cell_groups = FALSE,
# label_leaves = FALSE, label_branch_points = FALSE,graph_label_size = 4)
#p + geom_vline(xintercept = seq(-5,-4,0.25)) + geom_hline(yintercept = seq(3,4,0.25))
#embed <- data.frame(Embeddings(seurat, reduction = "umap"))
#embed <- subset(embed, UMAP_1 > -5 & UMAP_1 < -4.75 & UMAP_2 > 3& UMAP_2 < 3.25)
#root.cell <- rownames(embed)
#cds <- order_cells(cds, root_cells = root.cell)
#plot_cells(cds, color_cells_by = "pseudotime", label_cell_groups = FALSE,
# label_leaves = FALSE, label_branch_points = FALSE, graph_label_size = 4)
##寻找拟时轨迹差异基因,graph_test分析最重要的结果是莫兰指数（morans_I），其值在-1至1之间，0代表此基因没有
#空间共表达效应，1代表此基因在空间距离相近的细胞中表达值高度相似。#long time
#Track_genes <- graph_test(cds, neighbor_graph="principal_graph", cores=10)#take long time
#Track_genes<-read.csv("Trajectory_genes.csv", sep=",",row.names = 1)
#write.csv(Track_genes,"Trajectory_genes01.csv",row.names = TRUE)
#13 genes morans_I>0.6 compared with 166_immune_gene
Track<-c("FTL","IFNG","CCL5","CD27","TIGIT","CTLA4","TNFRSF9","CCR1","TNFRSF4")
plot_genes_in_pseudotime(cds[Track,], color_cells_by="assigned_cell_type", min_expr=0.5, ncol = 3)
#FeaturePlot图
#plot_cells(cds, genes=Track, show_trajectory_graph=FALSE,label_cell_groups=FALSE, label_leaves=FALSE)