rm(list = ls())
###############################input data
dir_path <- "C:\\Users\\liyix\\OneDrive\\Desktop\\"
dir_path_name <- dir(dir_path,pattern = ".*.csv",full.names = T)
dir_path_name
## [1] "C:\\Users\\liyix\\OneDrive\\Desktop\\pathways_number_stat_edge.csv"
## [2] "C:\\Users\\liyix\\OneDrive\\Desktop\\pathways_number_stat_node.csv"
#####################################node
node_1 <- read.csv(grep("pathways_number_stat_node.csv",dir_path_name,value = T),header = T,stringsAsFactors = F)
dim(node_1) #[1] 8 2
## [1] 8 2
node_1$cate <- "pathway"
node_1
## Var1 Freq cate
## 1 Carcinogenicity 51 pathway
## 2 Cardiotoxicity 20 pathway
## 3 Developmental toxicity 3 pathway
## 4 Hepatotoxicity 11 pathway
## 5 Nephrotoxicity 12 pathway
## 6 Neurotoxicity 13 pathway
## 7 Reproductive toxicity 12 pathway
## 8 Skin toxicity 101 pathway
#View(node_1)
colnames(node_1) <- c("name","Count","ONTOLOGY")
###############################edge
edge_1 <- read.csv(grep("pathways_number_stat_edge.csv",dir_path_name,value = T),header = T,stringsAsFactors = F)
dim(edge_1) #[1] 28 3
## [1] 28 3
colnames(edge_1) <- c("source","target","weight")
summary(edge_1)
## source target weight
## Length:28 Length:28 Min. :0.0000
## Class :character Class :character 1st Qu.:0.0000
## Mode :character Mode :character Median :0.0000
## Mean :0.7857
## 3rd Qu.:1.0000
## Max. :6.0000
edge_1
## source target weight
## 1 Nephrotoxicity Reproductive toxicity 6
## 2 Cardiotoxicity Nephrotoxicity 3
## 3 Cardiotoxicity Reproductive toxicity 3
## 4 Nephrotoxicity Skin toxicity 3
## 5 Developmental toxicity Nephrotoxicity 2
## 6 Developmental toxicity Reproductive toxicity 2
## 7 Cardiotoxicity Developmental toxicity 1
## 8 Cardiotoxicity Skin toxicity 1
## 9 Reproductive toxicity Skin toxicity 1
## 10 Carcinogenicity Cardiotoxicity 0
## 11 Carcinogenicity Developmental toxicity 0
## 12 Carcinogenicity Hepatotoxicity 0
## 13 Carcinogenicity Nephrotoxicity 0
## 14 Carcinogenicity Neurotoxicity 0
## 15 Carcinogenicity Reproductive toxicity 0
## 16 Carcinogenicity Skin toxicity 0
## 17 Cardiotoxicity Hepatotoxicity 0
## 18 Cardiotoxicity Neurotoxicity 0
## 19 Developmental toxicity Hepatotoxicity 0
## 20 Developmental toxicity Neurotoxicity 0
## 21 Developmental toxicity Skin toxicity 0
## 22 Hepatotoxicity Nephrotoxicity 0
## 23 Hepatotoxicity Neurotoxicity 0
## 24 Hepatotoxicity Reproductive toxicity 0
## 25 Hepatotoxicity Skin toxicity 0
## 26 Nephrotoxicity Neurotoxicity 0
## 27 Neurotoxicity Reproductive toxicity 0
## 28 Neurotoxicity Skin toxicity 0
###########################################################plot
#install.packages("igraph")
library(igraph)
##
## Attaching package: 'igraph'
## The following objects are masked from 'package:stats':
##
## decompose, spectrum
## The following object is masked from 'package:base':
##
## union
g <- graph_from_data_frame(d=edge_1, vertices=node_1, directed=FALSE)
#str(g)
show(g)
## IGRAPH 1904662 UNW- 8 28 --
## + attr: name (v/c), Count (v/n), ONTOLOGY (v/c), weight (e/n)
## + edges from 1904662 (vertex names):
## [1] Nephrotoxicity --Reproductive toxicity
## [2] Cardiotoxicity --Nephrotoxicity
## [3] Cardiotoxicity --Reproductive toxicity
## [4] Nephrotoxicity --Skin toxicity
## [5] Developmental toxicity--Nephrotoxicity
## [6] Developmental toxicity--Reproductive toxicity
## [7] Cardiotoxicity --Developmental toxicity
## [8] Cardiotoxicity --Skin toxicity
## + ... omitted several edges
#View(edge_1)
#tiff(filename=paste0(dir_path,"network_1.tif"),width = 20, height = 20, units = "cm",
# compression = "lzw",bg = "white", res = 300, family = "serif", restoreConsole = TRUE)
p1 <- plot(g, layout=layout_in_circle, main="",vertex.label.color="black",
vertex.label.dist=0, vertex.label.font =1,edge.curved=0,
vertex.label.cex = 1.5,vertex.label.family = "serif",
edge.color="gray70", vertex.color = categorical_pal(8))
legend(x =0, y = -1.2, legend=c("3 ", "200 "), pch = 21, bty = "n",col = "black",
pt.cex = c(7,9),horiz= T, x.intersp = 2.5,adj = 2,cex=1.5)
legend(x = -2.2, y = -1.2, legend=c("Number of pathways"),
pch=21, pt.bg="black", pt.cex=0, bty="n",horiz=TRUE,cex=1.5)
#dev.off()
########################################
par(mfrow=c(2, 3), mar=c(0,0,1,0))
plot(g, layout=layout_randomly, main="Random")
plot(g, layout=layout_in_circle, main="Circle")
plot(g, layout=layout_as_star, main="Star")
plot(g, layout=layout_as_tree, main="Tree")
plot(g, layout=layout_on_grid, main="Grid")
plot(g, layout=layout_with_fr, main="Force-directed")
#################################################category color_plot
#V(g)$size <- log(strength(g))
V(g)$size <- node_1$Count
E(g)$width <- edge_1$weight
#abs(scale(edge_1$weight))
#par(mar=c(.2,0.2,.2,.2))
V(g)$name
## [1] "Carcinogenicity" "Cardiotoxicity" "Developmental toxicity"
## [4] "Hepatotoxicity" "Nephrotoxicity" "Neurotoxicity"
## [7] "Reproductive toxicity" "Skin toxicity"
#dev.off()
#View(edge)
######################
p1
## NULL