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library(ggplot2)library(monocle3)source('./ks_run_monocle3.R')#monocle3 analysis#运行monocle3分析0参照monocle3视频教程cds_data <- ks_run_monocle3(object=cytotrace2_sce,idents="cluster",use_partition=F,learn_graph_control=list(minimal_branch_len=9.5,euclidean_distance_ratio=1),define_root=T,know_root=T,root_state="YSMP")#plot-拟时基本作图plot_cells(cds_data, label_cell_groups = F,color_cells_by = "pseudotime",label_branch_points = F,label_roots =F,label_leaves =F,graph_label_size = 0,cell_size=2,trajectory_graph_color='black',trajectory_graph_segment_size = 2)
pseudotime <- pseudotime(cds_data) %>% as.data.frame()pseudotime$cell <- rownames(pseudotime)colnames(pseudotime)[1] <- "peu"celltype <- cds_data@clusters$UMAP %>% as.data.frame()celltype$cell <- rownames(celltype)merge <-merge(pseudotime, celltype, by = 'cell')merge <- merge[order(merge$peu), ]
p=ggplot(merge,aes(peu,fill=clusters, color=clusters)) +geom_density(alpha = 0.5,size=1.2)+scale_fill_manual(values=c("#3F6F76", "#C65840", "#F4CE4B", "#62496F"))+ #设置颜色scale_color_manual(values=c("#3F6F76", "#C65840", "#F4CE4B", "#62496F"))+theme_classic()+ #我这里不展示坐标轴信息，可自行设置scale_y_continuous(expand = c(0,0))+theme(axis.line = element_blank(),axis.ticks.y=element_blank(),axis.title = element_blank(),axis.text.y = element_blank(),axis.text.x=element_text(colour='black',size=10))+labs(title = "Pseudotime")p
p+scale_y_break(c(1, 2),scales = c(0.5,2),expand=expansion(add = c(0, 0)),space = 0.2)
##或者加一个热图，使用AI将两者结合起来即可source('./ks_monocle3_heatmap.R')label genegenes <- c("C1QB","C1QC","C1QA","MRC1","LGMN","MS4A7","MAF","FOLR2","HLA-DPA1","CLEC10A","IL10RA","CD163","KCTD12","CLEC7A","MS4A6A","CD14","ITM2A","CYTL1","MDK","SELP","CD24","S100A8","S100A9","S100A12")ht2 = ks_monocle3_heatmap(cds = cds_data,graph_gene = plot_genes,celltype_color = c("#E69253", "#EDB931", "#E4502E", "#4f372d"),cluster_color =c("#8f657d", "#42819F", "#86AA7D", "#CBB396"),num_clusters=4,labels = T,label_genes = genes)
ggplot(merge, aes(x=peu,y=clusters,fill=clusters))+geom_density_ridges(scale=1) +scale_y_discrete(position = 'right')+theme_minimal()+theme(panel.grid = element_blank(),axis.title = element_blank(),axis.text = element_text(colour = 'black', size=8))+scale_x_continuous(position = 'top')+scale_fill_manual(values=c("#3F6F76", "#C65840", "#F4CE4B", "#62496F"))
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