KEGG_cluster for xiaodan

loading package

library(tidyverse)
## -- Attaching packages --------------------------------------- tidyverse 1.3.1 --
## v ggplot2 3.3.5     v purrr   0.3.4
## v tibble  3.1.6     v dplyr   1.0.8
## v tidyr   1.2.0     v stringr 1.4.0
## v readr   2.1.2     v forcats 0.5.1
## Warning: package 'tibble' was built under R version 4.1.3
## Warning: package 'tidyr' was built under R version 4.1.3
## Warning: package 'readr' was built under R version 4.1.3
## Warning: package 'dplyr' was built under R version 4.1.3
## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()
library(ggplot2)
library(ggthemes)
## Warning: package 'ggthemes' was built under R version 4.1.2
library(readxl)
## Warning: package 'readxl' was built under R version 4.1.3

settings

options(scipen = 200)
windowsFonts(HEL=windowsFont("Helvetica CE 55 Roman"),
             TNM=windowsFont("Times New Roman"),
             ARL=windowsFont("Arial"))
Sys.setenv(LANGUAGE = "en")

loading data

GO_KEGG <- read_excel("C:/Users/mjdee/Desktop/分子药理/GO_KEGG.xlsx")
KEGG_dataset <- GO_KEGG %>%
  dplyr::rename(enrichment=`Fold Enrichment`) %>% 
  arrange(desc(Count)) %>% 
  filter(Count >=10 & PValue<=0.01)

set theme

mytheme <- theme(axis.title=element_text(size=18,family = "TNM",colour = 'black',face = "bold"), 
                 axis.text=element_text(size=14,family = "TNM",colour = 'black',face = "bold"), 
                 axis.line = element_line(size=0.5, colour = 'black'), 
                 panel.background = element_rect(color='white'),
                 legend.key = element_blank() 
)

set plot details

p <- ggplot(KEGG_dataset,
            aes(x=enrichment,                 
                y=Term,colour=-1*log10(PValue),size=Count))+
  geom_point()+
  scale_size(range=c(4, 12))+
  scale_colour_gradient(low = "#5BBCD6",high = "#FF2500",space   = "Lab",na.value = "grey50",guide = "colourbar",
  aesthetics = "colour")+
  theme_gdocs()+
  ylab("KEGG Pathway Terms")+
  xlab("Fold Enrichment")+
  labs(color=expression(-log[10](PValue)))+
  theme(legend.title=element_text(size=14),legend.text = element_text(size=14,family = "TNM"))+
  theme(axis.title.y = element_text(margin = margin(r = 50)),axis.title.x = element_text(margin = margin(t = 20)))+
  theme(axis.text.x = element_text(face="bold",color="black",family = "TNM",angle=0,vjust=0))
p<- p+mytheme

plot show

plot(p)