单细胞marker基因展示之热图

##热图展示marker基因
1.seurat自带
scRNA1 <-  ScaleData(scRNA1,features = rownames(scRNA1))
cells = subset(scRNA1,downsample=300)##取其中的300个细胞，为了图好看
top10 <- marker %>% 
  #  filter(cluster!="other") %>%
  group_by(cluster) %>% 
  top_n(10, avg_log2FC) 

DoHeatmap(cells,features = top10$gene,size = 3,
  label = F,slot = "scale.data")+scale_fill_gradientn(colors = c("#4DBBD5","white","#E64B35"))
?DoHeatmap
ggsave(filename=paste0(pro,'DoHeatmap_check_top3_markers_by_clusters-2.pdf') ,
       width=10,height=8)

#用pheatmap画
library(pheatmap)
colanno=cells@meta.data 
colanno$celltype=factor(colanno$celltype,levels = unique(colanno$celltype))
colanno1=colanno[,6]
colanno1=as.data.frame(colanno1)
rownames(colanno1)=rownames(colanno)
colnames(colanno1)="celltype"
##先对细胞进行排序，按照celltype的顺序，然后对基因排序
rowanno=top10
colnames(top10)
rowanno=rowanno%>%arrange(cluster)
##提取scale矩阵的行列时，按照上面的顺序
mat4=cells[["RNA"]]@scale.data[rowanno$gene,rownames(colanno1)]
mat4[mat4>=2.5]=2.5
mat4[mat4 < (-1.5)]= -1 #小于负数时，加括号！

pheatmap(mat4,cluster_rows = F,cluster_cols = F,
         show_colnames = F,
         scale= "row",
         annotation_col = colanno1,
         gaps_row=as.numeric(cumsum(table(rowanno$cluster))[-6]),
         gaps_col=as.numeric(cumsum(table(colanno$celltype))[-6]) 
         
)
##cumsum(x) ：返回 x 向量的累计和
?pheatmap
##保存为pdf
pheatmap(mat4,cluster_rows = F,cluster_cols = F,
         show_colnames = F,
         annotation_col = colanno1,
         gaps_row=as.numeric(cumsum(table(rowanno$cluster))[-6]),
         gaps_col=as.numeric(cumsum(table(colanno$celltype))[-6]) ,
         filename="marker.heatmap.pdf",width=11,height = 7
)