绘制气泡图：单个轴上的所有路径项

Question

这是我的示例数据

a <- dput(head(df))
structure(list(Term = c("Reactome Gene Sets", "GO Biological Processes", 
"GO Biological Processes", "GO Biological Processes", "GO Biological Processes", 
"GO Biological Processes"), Pathway = c("R-MMU-191273", "GO:0034341", 
"GO:0050900", "GO:0046942", "GO:0001817", "GO:0048871"), VVV = c("Cholesterol biosynthesis", 
"response to interferon-gamma", "leukocyte migration", "carboxylic acid transport", 
"regulation of cytokine production", "multicellular organismal homeostasis"
), p_value = c(-11.6414922875, -9.3148301923, -6.2150336681, 
-5.9190690396, -5.8467499202, -5.767770517)), row.names = c(NA, 
-6L), class = c("tbl_df", "tbl", "data.frame"))

我在这里尝试显示路径及其各自的 pvalue

我的代码

ggplot(df, aes(x=Term,y=p_value)) +
  geom_point(aes(size=abs(p_value))) +
  #geom_text(data=df,label=df$Pathway) + 
  geom_label_repel(aes(label=Pathway), size=3)+
  
  #scale_color_gradientn(colours = rainbow(5)) +
  labs(
    x='-log10(pvalue)', y=NULL,
    color='p_value',size='pvalue'
  ) +
  theme(
    axis.title = element_text(face='bold'),
    axis.text = element_text(face='bold')
  )

我得到的输出是这个

有没有办法让我也可以将 Reactome 基因设置在与 GO 生物过程相同的轴或线上。我的想法是在一行中显示所有这些，显着的 pvalue 显示更大的气泡。

任何建议或帮助将不胜感激。

Answer 1

您可以根据Pathway 值应用nudge_x。

library(ggplot2)
library(ggrepel)
library(dplyr)

ggplot(df, aes(x=Term,y=p_value)) +
  geom_point(aes(size=abs(p_value))) +
  geom_label_repel(aes(label=Pathway), size=3, 
                   nudge_x = ifelse(grepl('R-MMU', df$Pathway), 1, 3),
                   direction = "y") +
  
  #scale_color_gradientn(colours = rainbow(5)) +
  labs(
    x='-log10(pvalue)', y=NULL,
    color='p_value',size='pvalue'
  ) +
  theme(
    axis.title = element_text(face='bold'),
    axis.text = element_text(face='bold')
  )

---

让所有东西都在同一个 X 轴上：

df %>%
  mutate(X_value = '-log10(pvalue)') %>%
  ggplot(aes(x=X_value,y=p_value)) +
  geom_point(aes(size=abs(p_value))) +
  geom_label_repel(aes(label=Pathway), size=3) +
  labs(y=NULL, x = NULL,color='p_value',size='pvalue')