如何在R中创建路径丰富热图？

Question

我有一些类似如下的数据：

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dput(Int)

structure(list(ID = c("GO", "GO", "GO", "Kegg", "Reactome", "Reactome", 
"GO", "GO", "GO", "GO", "Reactome", "GO", "Reactome", "GO", "Kegg", 
"Kegg"), Description = c("regulation of developmental growth", 
"cell maturation", "cell-substrate adhesion", "MAPK signaling pathway", 
"MET activates PTK2 signaling", "Signaling by MET", "growth factor binding", 
"canonical Wnt signaling pathway", "regulation of cellular response to growth factor stimulus", 
"regulation of cell cycle G2/M phase transition", "Glycolysis", 
"cell cycle DNA replication", "Signaling by EGFR", "stem cell differentiation", 
"Ras signaling pathway", "Calcium signaling pathway"), GeneRatio = c("6/62", 
"4/62", "26/224", "15/136", "8/144", "8/144", "13/220", "10/151", 
"14/151", "10/332", "33/2605", "26/3798", "20/2605", "7/62", 
"15/213", "15/213"), BgRatio = c("347/18670", "177/18670", "354/18670", 
"438/10971", "30/10654", "79/10654", "137/17696", "335/18670", 
"292/18670", "213/18670", "71/10654", "71/18670", "49/10654", 
"257/18670", "337/10971", "288/10971"), pvalue = c(0.001010736, 
0.002839063, 1.57e-13, 0.000338402, 4.17e-09, 1.06e-05, 1.64e-08, 
0.000406096, 1.11e-07, 0.004942, 4.17e-05, 0.001096187, 0.008292794, 
2.23e-05, 0.002389972, 0.00049388), p.adjust = c(0.031471355, 
0.047398143, 4.9e-11, 0.00342914, 9.91e-08, 0.00018386, 8.97e-07, 
0.034667052, 0.000278314, 0.038642228, 0.000242305, 0.011469503, 
0.029134446, 0.015875363, 0.03632758, 0.015479437), qvalue = c(0.024333169, 
0.036647518, 3.88e-11, 0.002920943, 8.26e-08, 0.000153301, 7.72e-07, 
0.030920283, 0.000248234, 0.030524074, 0.000156277, 0.0094808, 
0.018790567, 0.012274587, 0.029015103, 0.012363539), Count = c(6L, 
4L, 26L, 15L, 8L, 8L, 13L, 10L, 14L, 10L, 33L, 26L, 20L, 7L, 
15L, 15L), Subtypes = c("GroupA", "GroupA", "GroupB", "GroupB", 
"GroupB", "GroupB", "GroupB", "GroupB", "GroupB", "GroupB", "GroupB", 
"GroupB", "GroupB", "GroupC", "GroupC", "GroupC"), Cluster = c("Cluster1", 
"Cluster1", "Cluster2", "Cluster2", "Cluster2", "Cluster2", "Cluster2", 
"Cluster3", "Cluster3", "Cluster3", "Cluster4", "Cluster4", "Cluster4", 
"Cluster1", "Cluster5", "Cluster5")), row.names = c(NA, -16L), class = "data.frame")

我用下面的代码创建了一个点图：

library(ggplot2)
library(forcats)
library(dplyr)

Int2 <- Int[order(Int$Cluster, decreasing = FALSE),]
Int2$Description <- factor(Int2$Description, levels=Int2$Description[order(Int2$Cluster)])

p <- ggplot(Int2, aes(x = Count, y = Description)) + 
  geom_point(aes(size = Count, color = p.adjust)) +
  theme_bw(base_size = 14) +
  theme(axis.text=element_text(size=15, face = "bold", color = "black"),
        axis.title=element_text(size=15, face = "bold", color = "black")) +
  scale_colour_gradient(limits=c(0, 0.10), low="red") +
  ylab(NULL)

p1 <- p + facet_grid(.~Subtypes, scale = "free") +
  theme(strip.text.x = element_text(size = 15, colour = "black", face = "bold"))

但我感兴趣的是创建一个路径丰富热图，显示y轴上的路径和顶部的集群，还在图的右侧显示子类型。

它应该看起来像这样：

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Answer 1

像这样的东西可能会让你更接近你正在寻找的东西，但我想知道像{gt}包这样的东西是否更容易将事情转化为表格格式……

axis_text_colors <- case_when(Int2$ID == "GO" ~ "blue", 
                              Int2$ID == "Kegg" ~ "purple", 
                              Int2$ID == "Reactome" ~ "green")

ggplot(Int2) + 
  aes(x = Cluster, y = Description) + 
  facet_grid(Subtypes ~ ., space = "free_y", scale = "free_y") +
  geom_tile(aes(fill = p.adjust)) +
  # scale_fill_gradient(limits=c(0, 0.10), low="red") +
  labs(
    x = NULL, 
    y = NULL
  ) + 
  theme(
    axis.text.x = element_text(angle = 90), 
    axis.text.y = element_text(color = axis_text_colors)
  ) +
  NULL