zzov_fig4F&H.Rmd

---
title: "Untitled"
author: "yuyi"
date: "2022/2/11"
output: html_document
---

```{r }
```



```{r }
rm(list = ls())
# source("D:/library_yu.R")
library(openxlsx)
df <- read.xlsx("20220211ZZOV_univariateCox_plasma_tissue.xlsx")
df1 <- read.xlsx("data.xlsx")
# library(readxl)
library(tidyverse)
library(ggplot2)
library(ggrepel)
-log2(df$plasmalikelihood.pvalue)
pdf(file='sand2.pdf',height =  4,width = 8)
ggplot()+
  layer(data=df,mapping = aes(x=label1_x,y=label1_y,colour=pathway,size=-log2(plasmalikelihood.pvalue)),geom="point",stat = "identity",position = "identity",params=list(alpha=.6,size=-log2(df$plasmalikelihood.pvalue)))+
  geom_text_repel(data=df,mapping = aes(x=label1_x,y=label1_y,label = df$gene_name),size=3)+
  layer(data=df1,mapping = aes(x=label2_x1,y=label2_y1),geom="point",params=list(color="blue",alpha=.3,shape=3),stat="identity", position = "identity")+
  geom_hline(aes(yintercept=1),linetype=5,col="grey")+
  geom_vline(aes(xintercept = 1),linetype=5,col="grey")+
  scale_y_continuous()+
  scale_x_continuous()+
  coord_cartesian()+
  theme_classic()
 dev.off()
 
 
 
```



```{r }

bar <- read.xlsx("./bar.xlsx")

#install.packages("DescTools")
library(DescTools)


 head(bar)

 
 pdf(file='bar.pdf',height =  4,width = 10)
PlotPyramid(lx=bar[,"LogP1(-)"], 
            rx=bar[,"LogP2(-)"],
            ylab=bar$Description,
            col=c("lightslategray", "orange2"),
            border = NA, ylab.x=0,
            xlim=c(-30,15),
            gapwidth = NULL, 
            cex.lab = 0.8, cex.axis=0.8, 
            xaxt = TRUE,
            lxlab="-LogP(UP)", 
            rxlab="-LogP(FP)",
            main="bar plot",
            space=0.5, args.grid=list(lty=1))

 dev.off()


#  library(scales)
show_col(hue_pal()(6))
#  
hue_pal()(5)
 
 
 library(plotrix)
 
 UP<-bar$`LogP1(-)`
 FP<-bar$`LogP2(-)`
 
 UCOL<-c("#A3A500" ,"lightslategray","#00B0F6","#00BF7D","lightslategray")
 FCOL<-c("orange2","orange2","orange2","#F8766D" ,"#E76BF3")
 
 labels<-bar$Description
 pdf(file='bar.pdf',height =  4,width =10)
 par(mar=pyramid.plot(UP,FP,labels = labels, main="bar plot",lxcol=UCOL,rxcol = FCOL,gap=0,show.values = T,top.labels = c("FP","Description","UP"),unit = "-LogP",laxlab=c(0,10,20,30),raxlab=c(0,5,10,15)))
 dev.off()


 
# 6 #F8766D  #B79F00 #00BA38 #00BFC4 #619CFF #F564E3
#  library(scales)
# show_col(hue_pal()(n))
#  
# 5  #F8766D
 
```