富集分析可视化-高级教程

GO富集分析可视化

先上代码

rm(list = ls())
library(openxlsx)
library(tidyverse)
library(ggplot2)


data=read.xlsx("salmon_GOKEGG.xlsx",sheet=2)
names(data)
GO_pink<- data %>% dplyr::filter(.,FDR < 0.05 & Count >= 4)# & (type == "BP" | type == "MF" | type == "CC"))
names(GO_pink)

table(GO_pink$Category)
# 
GO_pink <- within(GO_pink, type <- factor(Term, levels = c("BP", "CC", "MF", "KEGG")))
with(GO_pink, levels(type))
GO_pink <- within(GO_pink, Category <- factor(Module, levels = c("Salmon","Blue")))
with(GO_pink, levels(Category))



windowsFonts(myFont = windowsFont("Times New Roman"))
tiff(filename = "salmon+blue_GO.tiff",
     width = 8,
     height = 6,
     units = "in",
     pointsize = 5,res = 300)
ggplot2::ggplot(GO_pink,aes(FDR,
                            Description,
                            size=Count,
                            color=-log10(FDR)))+
  geom_point()+
  facet_grid(vars(type),vars(Category),shrink = TRUE,scales = "free_y",space="free")+
  #theme(strip.background = element_rect(color="#FC4E07", fill=c("salmon","blue"), 
                                        #size=1.5, linetype="solid"))+
  #facet_wrap(~type)+
  #facet_wrap(~type,scales="free")+
  scale_color_gradient(low="green",high = "red")+
  theme_bw()+
  scale_y_discrete(labels = function(x) str_wrap(x, width = 50) )+
  theme(axis.title.x = element_text(size = 8,
                                    color = "black",
                                    face = "bold", 
                                    vjust = 0, 
                                    hjust = 0.5, 
                                    angle = 0,
                                    family = "myFont"))+
  theme(axis.title.y = element_text(size = 12,
                                    color = "black",
                                    face = "bold", 
                                    vjust = 0.5, 
                                    hjust = 0.5, 
                                    angle = 90,
                                    family = "myFont"))+
  theme(axis.text.y = element_text(size = 12,
                                   color = "black",
                                   face = "plain", 
                                   vjust = 0.5, 
                                   hjust = 1, 
                                   angle = 0,
                                   family = "myFont"))+
  theme(axis.text.x = element_text(size = 10,
                                   color = "black",
                                   face = "plain", 
                                   vjust = 0.5, 
                                   hjust = 0.5, 
                                   angle = 60,
                                   family = "myFont"))+
  theme(legend.text =  element_text(size = 8,
                                    color = "black",
                                    face = "plain", 
                                    vjust = 0, 
                                    hjust = 0, 
                                    angle = 0,
                                    family = "myFont"))+
  theme(legend.title  =  element_text(size = 8,
                                      color = "black",
                                      face = "plain", 
                                      vjust = 0, 
                                      hjust = 0, 
                                      angle = 0,
                                      family = "myFont"))
#theme(strip.placement = "outside")
#theme(strip.text.x = element_text(size = 30, colour = "#FC0043")) + # 设置分面的字字体大小、颜色、背景、边框，
#theme(strip.text.y = element_text(size = 15, colour = "#60FC00")) +
#theme(strip.switch.pad.grid = unit(1, "inch")) # 设置分面条带与坐标轴的距离
dev.off()