如何在 R 中创建 Pathway Enrichment 热图？

Question

我有如下一些数据：

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")

我使用以下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"))

但我有兴趣创建一个通路富集热图，在 y 轴上显示通路，在顶部显示集群，并在图的右侧显示子类型。

它应该是这样的：

Answer 1

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把东西变成 table 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

如何在 R 中创建 Pathway Enrichment 热图？

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