单细胞小提琴图

4BPY(OOQ%IXO29{`L}7K2%5.png

#############差异小提琴图
tumor <- readRDS("tumor.RDS")
df.data <- tumor@assays$RNA@data %>% as.data.frame()
head(rownames(df.data))
Cs <- df.data["Cs",] %>% as.data.frame()%>% t() %>% as.data.frame()
Cs$id<-rownames(Cs)


####提取样本id
cell <- as.data.frame([email protected])
cell$id<-rownames(cell)
cell<-cell[,c("id","tissue_type")]


count<-merge(Cs,cell,by="id")

###############小提琴图
# 添加P值
# 得到cluster6和cluster10中的gsva score 最大值
count.geneset.group1 <- count$geneset[count$tissue_type == "test"]
count.geneset.group2 <- count$geneset[count$tissue_type == "control"]

# 确定P值添加的位置
ysegment1 <- max(count.geneset.group1)
ysegment2 <- max(count.geneset.group2)
ysegment.max <- max(ysegment1, ysegment2)

# 根据P值确定加几颗星
pval <- 2.065159e-74

if (pval < 0.001) {
  pval.label = "***"
} else if (pval < 0.005) {
  pval.label = "**"
} else if (pval < 0.05) {
  pval.laben = "*"
} else if (pval >= 0.05) {
  pval.label = "non.sig"
}

# 自定义颜色
blue <- "#619CD6"
green <- "#89C32E"
p <- ggplot(count, aes(x = tissue_type, y = Cs, fill = tissue_type)) +
  geom_violin() +
  geom_boxplot(size=0.5,width=0.1,color="white") +
  scale_fill_manual(values = c(blue, green)) + # 用自定义颜色填充
  theme_classic() +
  theme(panel.grid = element_blank(), 
        plot.margin = margin(0.5, 0.5, 0.5, 0.5, "cm"), 
        axis.title.x = element_text(color = "black", size = 20), 
        axis.title.y = element_blank(), 
        axis.text = element_text(color = "black", size = 16), 
        axis.line = element_line(colour = "black", size = 0.6), 
        plot.title = element_text(size = 20, hjust = 0.5)) + 
  # 添加图形标题
  ggtitle("Cs") +
  guides(fill = F)
p


# 前面已经得到了pvalue,添加上去就可以了
# 确定P值添加的位置
ysegment1 <- max(count.geneset.group1)
ysegment2 <- max(count.geneset.group2)
ysegment.max <- max(ysegment1, ysegment2)

ysegment1 <- 3.5
ysegment2 <- 3.5
ysegment.max <-3.5

p + 
  # 图形中的一个横线和两个竖线
  #annotate("segment", x = 1, xend = 2, y = ysegment.max + 0.02, yend = ysegment.max + 0.02) + 
  #annotate("segment", x = 1, xend = 1, y = ysegment1 + 0.01, yend = ysegment.max + 0.02) +
  #annotate("segment", x = 2, xend = 2, y = ysegment2 + 0.01, yend = ysegment.max + 0.02) +
  # 添加P值对应的星号
  annotate("text", 
           size = 8, # *的大小
           x = 1.5, 
           y = ysegment.max - 0.03, #可以微调*所在的位置
           label = pval.label)

ggsave("Cs.tumor.all.pdf",width = 10,height = 10)