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r - 如何在 R 中创建 Pathway Enrichment 热图？

问题描述

我有一些数据如下：

在此处输入图像描述

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，显示 y 轴上的通路和顶部的簇，并在图的右侧显示子类型。

它应该看起来像这样：

在此处输入图像描述

标签： rggplot2heatmapggpubr

解决方案

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把东西变成表格格式......

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

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