用ggplot2 R显示背景中其他颜色的火山图点

Question

我编写了下面的代码来创建一个火山图，它是基于data.frame "gseaRes“的变量"group”着色的。有色点指的是我感兴趣的路径，而其他(不感兴趣的)路径应该是灰色的，在背景中。我使用geom_point中的参数"alpha“来使其更透明，但灰色点在灰色点内总是模糊不清，灰色点很难被看到，所以我们不知道它们是多少。我在徘徊，如果有人知道如何将这些点分为两层，一层对另一层，就像我们对顶部的散点图和线条所做的那样。有参数吗?还是用另一种方式编码？

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下面是我使用的数据集：https://github.com/mariakondili/GSEA/blob/main/GSEA_dataframe.tsv

下面是我制作它的方法：

suppressPackageStartupMessages(library(tidyverse)) 

gseaRes %>%  
mutate("group" = ifelse(str_detect(pathway,"blabla1"),"group1",
                                    ifelse(str_detect(pathway,"blabla2"), "group2",   
                                    ifelse(str_detect(pathway,"blabla3"), "group3",
                                    ifelse(str_detect(pathway,"blabla4"), "group4",
                                    ifelse(str_detect(pathway,"blabla5"),"group5","Other"))))))



ggplot(gseaRes , aes(x=-log10(padj), y=NES, size=size, col=group)) +
geom_point(alpha=ifelse(gseaRes$group=="Other",0.02, 1)) +
scale_color_manual(values = c("group1" = "violetred",
                              "group2" = "royalblue1" ,
                              "group3"="orange", 
                               "group4" = "cyan",
                               "group5" ="tomato4",
                               "Other" = "grey30")) + theme_classic()

Answer 1

您可以使用两个传递筛选数据集的geom_point，一个只包含“其他”类别，一个包含您感兴趣的路径：

library(tidyverse)

gseaRes <- read_tsv("https://raw.githubusercontent.com/mariakondili/GSEA/main/GSEA_dataframe.tsv")

gseaRes <- gseaRes %>%
  mutate(group = ifelse(str_detect(pathway, "_ACTIN"), "group1",
    ifelse(str_detect(pathway, "blabla"), "group2",
      ifelse(str_detect(pathway, "blabla"), "group3",
        ifelse(str_detect(pathway, "blabla"), "group4",
          ifelse(str_detect(pathway, "blabla"), "group5", "Other")
        )
      )
    )
  ))

ggplot(gseaRes, aes(x = -log10(padj), y = NES, size = size, col = group)) +
  geom_point(data = filter(gseaRes, group == "Other"), alpha = .02) +
  geom_point(data = filter(gseaRes, !group == "Other")) +
  scale_color_manual(values = c(
    "group1" = "violetred",
    "group2" = "royalblue1",
    "group3" = "orange",
    "group4" = "cyan",
    "group5" = "tomato4",
    "Other" = "grey30"
  )) +
  theme_classic()

​

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