在 R 中重现此图 - 编程之家

如何解决在 R 中重现此图

我有两组患者。我想为两组患者绘制一个情节

类似这个情节

我有这样的数据

> dput(df)
structure(list(gene = c("18q","4q","21p","21q","5q","22q","17p","3p","9p","4p","9q","19q","10q","15q","16p","19p","1p","18p","16q","8p","18q","14q","20q"),CNV = c("Deletion","Deletion","Amplification"),log10_pvalue = c(5.974694135,5.73754891,4.995678626,4.970616222,4.793174124,4.109020403,3.524328812,2.823908741,2.567030709,2.186419011,1.769551079,1.59345982,1.416801226,1.195860568,1.094743951,1.087777943,4.083019953,3.826813732,2.675717545,2.342944147,2.084072788,1.850780887,1.659555885,1.197226275,1.88941029),Percentage_altered = c(0.61,0.53,0.61,0.56,0.44,0.5,0.47,0.39,0.28,0.33,0.31,0.22,0.36,0.63,0.52,0.59,0.67,0.26,0.48,0.3,0.5
),group = c("Non-responders","Non-responders","Responders","Responders"
)),class = "data.frame",row.names = c(NA,-34L))
>

我已经尝试过这个代码，但没有给我你产生的结果

df %>%
  mutate(net_frequency=ifelse(CNV == "Deletion",-Percentage_altered/100,Percentage_altered/100)) %>%
  crossing(.,tibble(grp = c("Responders","Non-Responders"))) %>%
  mutate(log10_pvalue = if_else(CNV == "Deletion",-log10_pvalue,log10_pvalue)) %>% 
  ggplot(aes(x = log10_pvalue,y = net_frequency,color = log10_pvalue)) +
  geom_point(aes(size=Percentage_altered)) +
  geom_text_repel(aes(label=ifelse(log10_pvalue > -log10(0.05),gene,"")),force=10) +
  geom_hline(yintercept=0,lty=2) +
  scale_color_distiller(type = "div") +
  theme_classic() +
  facet_wrap(~grp)

我得到了这样的情节但没有意义

如果您看一下，对于这两个组，仅绘制了响应者的信息

你能帮忙编辑代码吗

解决方法

正如@andrew_reece 所建议的那样，facet_* 会在这里提供帮助。

由于我们在数据中没有任何“响应者”的概念，我将使用 tidyr::crossing 盲目复制数据。

此外，为了演示，我删除了 theme_classic 以突出显示窗格。（使用没有问题，我只是想说清楚区别。）

library(dplyr)
library(ggplot2)
library(ggrepel) # geom_text_repel
library(tidyr)   # crossing
df %>%
  mutate(net_frequency=ifelse(CNV == "Deletion",-Percentage_altered/100,Percentage_altered/100)) %>%
  crossing(. tibble(resp = c("Responder","Non-Responder"))) %>%
  ggplot(. aes(x=log10_pvalue,y=net_frequency)) +
  geom_point(aes(size=Percentage_altered,color=log10_pvalue)) +
  geom_text_repel(aes(label=ifelse(log10_pvalue > -log10(0.05),gene,"")),force=10) +
  geom_hline(yintercept=0,lty=2) +
  facet_wrap(. ~ resp)

至于“两组不同颜色”，你需要什么并不是很清楚。如果您希望（例如）响应者的色标为“蓝色”，非响应者的色标为“红色”，请查看 ggplot 扩展包，例如 ggnewscale 或 ggrelayer。（它们不是烘焙的。）

更新包括 OP 的更新数据，现在有两个组。
编辑 2 根据评论删除 OP 的原始 geom_repel 过滤器。

这是一种通过将 CNV == 'Deletion' 的所有 log10_pvalue 值设为负数来创建发散色标的方法。与 facet_wrap() 搭配使用，即可实现您的目标。

df %>% 
  mutate(net_frequency=ifelse(CNV == "Deletion",Percentage_altered/100),log10_pvalue = if_else(CNV == "Deletion",-log10_pvalue,log10_pvalue)) %>% 
  ggplot(aes(x = log10_pvalue,y = net_frequency,color = log10_pvalue)) +
  geom_point(aes(size=Percentage_altered)) +
  geom_text_repel(aes(label=gene),lty=2) +
  scale_color_distiller(type = "div") +
  theme_classic() +
  facet_wrap(~group)