seurat自己的vlnplot出的圖感覺有點(diǎn)丑丑的，網(wǎng)上找到了scRNAseq || 堆疊小提琴圖(StackedVlnPlot)的4種實(shí)現(xiàn)方式。這個(gè)教程基本實(shí)現(xiàn)了我想要堆疊小提琴圖的效果。同時(shí)也推一下他們的微信公眾號(hào)上教程：R函數(shù)實(shí)現(xiàn)單細(xì)胞StackedVlnPlot.
不過，我在實(shí)際使用的過程種遇到了一點(diǎn)小問題。
他們的原始代碼為：

library(Seurat)
library(ggplot2)

modify_vlnplot<- function(obj,
                          feature,
                          pt.size = 0,
                          plot.margin = unit(c(-0.75, 0, -0.75, 0), "cm"),
                          ...) {
  p<- VlnPlot(obj, features = feature, pt.size = pt.size, ... )  +
    xlab("") + ylab(feature) + ggtitle("") +
    theme(legend.position = "none",
          axis.text.x = element_blank(),
          axis.text.y = element_blank(),
          axis.ticks.x = element_blank(),
          axis.ticks.y = element_line(),
          axis.title.y = element_text(size = rel(1), angle = 0, vjust = 0.5),
          plot.margin = plot.margin )
  return(p)
}

## main function
StackedVlnPlot<- function(obj, features,
                          pt.size = 0,
                          plot.margin = unit(c(-0.75, 0, -0.75, 0), "cm"),
                          ...) {
  
  plot_list<- purrr::map(features, function(x) modify_vlnplot(obj = obj,feature = x, ...))
  plot_list[[length(plot_list)]]<- plot_list[[length(plot_list)]] +
    theme(axis.text.x=element_text(), axis.ticks.x = element_line())
  
  p<- patchwork::wrap_plots(plotlist = plot_list, ncol = 1)
  return(p)
}

#函數(shù)調(diào)用
mycols <- c(brewer.pal(n = 9, name = 'Set1'),
            brewer.pal(n = 8, name = 'Set2'),
            brewer.pal(n =11, name = 'Set3'),
            brewer.pal(n =8, name = 'Accent'),
            brewer.pal(n =8, name = 'Dark2'),
            brewer.pal(n =12, name = 'Paired'),
            brewer.pal(n =9, name = 'Pastel1'),
            brewer.pal(n =8, name = 'Pastel2'))
#mycols2 <- names(sort(table(mycols ))[sort(table(mycols )) == 1])
mycols <- mycols[mycols %in% names(sort(table(mycols ))[sort(table(mycols )) == 1])]

StackedVlnPlot(lmg02P, c('CD3D', 'GZMB','CD68','CD163', 'KRT18','KRT19','EPCAM'), pt.size=0, cols=mycols)

得到的結(jié)果示例：

image.png

可以看到有2個(gè)小問題：

• 坐標(biāo)軸的問題沒有旋轉(zhuǎn)
• patchwork的拼圖沒有很緊湊，導(dǎo)致多個(gè)gene進(jìn)行堆疊的時(shí)候，顯得很空，導(dǎo)致不適合很多基因一起作圖

基于上面的小問題，修改了一下上面的函數(shù)。

#self modify for more compact.
modify_vlnplot <- function(obj, feature, pt.size = 0, plot.margin = unit(c(-0.75, 0, -0.75, 0), "cm"),...) {
  p <- VlnPlot(obj, features = feature, pt.size = pt.size, ... ) +
    theme_void() +
    ylab(feature) +
    theme(legend.position = 'none',
          plot.margin = plot.margin,
          title = element_blank(),
          axis.title.y = element_text(hjust = 0.5, angle = 0)
          )
  return(p)
}



## main function
StackedVlnPlot <- function(obj, features, pt.size = 0, plot.margin = unit(c(-0.75, 0, -0.75, 0), "cm"), ...) {
  plot_list <- purrr::map(features, function(x) modify_vlnplot(obj = obj,feature = x, ...))
  plot_list[[length(plot_list)]]<- plot_list[[length(plot_list)]] +
    theme(axis.text.x=element_text(angle = 90), axis.ticks.x = element_line())
  p <- patchwork::wrap_plots(plotlist = plot_list, ncol = 1)
  return(p)
}
#函數(shù)調(diào)用
mycols <- c(brewer.pal(n = 9, name = 'Set1'),
            brewer.pal(n = 8, name = 'Set2'),
            brewer.pal(n =11, name = 'Set3'),
            brewer.pal(n =8, name = 'Accent'),
            brewer.pal(n =8, name = 'Dark2'),
            brewer.pal(n =12, name = 'Paired'),
            brewer.pal(n =9, name = 'Pastel1'),
            brewer.pal(n =8, name = 'Pastel2'))
#mycols2 <- names(sort(table(mycols ))[sort(table(mycols )) == 1])
mycols <- mycols[mycols %in% names(sort(table(mycols ))[sort(table(mycols )) == 1])]

StackedVlnPlot(lmg02P, c('CD3D', 'GZMB','CD68','CD163', 'KRT18','KRT19','EPCAM'), pt.size=0, cols=mycols)

修改后的畫圖后的示例：

image.png

注意，部分標(biāo)簽信息已經(jīng)隱去。
可以看到修改的圖更加緊湊，可以用于大量marker gene的繪制。