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玩转单细胞(16)：Scanpy单细胞h5ad数据转化为Seurat对象
library(Seurat)library(dplyr)library(ggplot2)library(ggrepel)#===============================================================================#UMAP plotemb <- Embeddings(obj,reduction = 'umap') %>% #提取坐标数据as.data.frame() %>%mutate(clusters=obj@meta.data$seurat_clusters,#添加cell注释信息celltype=obj@meta.data$celltype)#ggplot作图ggplot(emb, aes(UMAP_1,UMAP_2))+geom_point(aes(colour = clusters), size=0.5)+#颜色选择clustertheme_classic()+theme(axis.text = element_text(color = 'black', size = 10))+scale_color_manual(values = c("#edc951","#eb6841","#cc2a36","#4f372d","#00a0b0","#7A989A", "#849271", "#CF9546", "#C67052", "#C1AE8D","#3F6F76", "#C65840", "#F4CE4B", "#62496F", "#69B7CE","#A4B7E1", "#B8B87A"))#修改颜色
label <- emb %>%group_by(celltype) %>%summarise(UMAP_1 = median(UMAP_1),UMAP_2 = median(UMAP_2))%>%as.data.frame()ggplot(emb, aes(UMAP_1,UMAP_2))+geom_point(aes(colour = clusters), size=0.5)+#颜色选择clustertheme_classic()+theme(axis.text = element_text(color = 'black', size = 10))+scale_color_manual(values = alpha(c("#edc951","#eb6841","#cc2a36","#4f372d","#00a0b0","#7A989A", "#849271", "#CF9546", "#C67052", "#C1AE8D","#3F6F76", "#C65840", "#F4CE4B", "#62496F", "#69B7CE","#A4B7E1", "#B8B87A"),0.5))+geom_text(data = label[label$celltype %in% c("Muscle",'Fibroblasts','Endothlial'),],aes(UMAP_1,UMAP_2, label=celltype),nudge_y = 4,color = 'black',size = 4) +geom_text(data = label[label$celltype %in% c("T cells",'Mast cells','Melanocytes','Lymphatic'),],aes(UMAP_1,UMAP_2, label=celltype),nudge_y = 2,color = 'black',size = 4) +geom_text(data = label[label$celltype %in% c("Keratinocytes"),],aes(UMAP_1,UMAP_2, label=celltype),nudge_y = 2,nudge_x = 5,color = 'black',size = 4) +geom_text(data = label[label$celltype %in% c('Myeloid'),],aes(UMAP_1,UMAP_2, label=celltype),nudge_y = 4,color = 'black',size = 4) +NoLegend()
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