rm(list = ls())
#1.1 input data
dir_path <- "C:\\Users\\liyix\\OneDrive\\Desktop\\data\\"
dir_path_files <- list.files(pattern = ".csv",dir_path,recursive = T,all.files = T,full.names = T)
dir_path_files #
## [1] "C:\\Users\\liyix\\OneDrive\\Desktop\\data\\2022-07-01-data_edge.csv"
## [2] "C:\\Users\\liyix\\OneDrive\\Desktop\\data\\2022-07-01-data_node.csv"
data_edge_1 <- read.csv(grep("2022-07-01-data_edge.csv",dir_path_files,value = T),header = T,stringsAsFactors = F)
data_node <- read.csv(grep("2022-07-01-data_node.csv",dir_path_files,value = T),header = T,stringsAsFactors = F)
data_node <- data_node[c(1:3,9:20), ]
data_edge_1 <- data_edge_1[data_edge_1$invivo %in% data_node$node, ]
data_edge_1 <- data_edge_1[data_edge_1$SYMBOL %in% data_node$node, ]
data_node; data_edge_1
## node number col
## 1 Carcinogenicity 1 1
## 2 Neurotoxicity 1 2
## 3 Nephrotoxicity 1 3
## 9 AHR 1 9
## 10 FASLG 1 9
## 11 BCL2 1 9
## 12 BRCA1 1 9
## 13 MAPK14 1 9
## 14 ESR1 1 9
## 15 GSTM1 1 9
## 16 H2AX 1 9
## 17 HIF1A 1 9
## 18 HMOX1 1 9
## 19 IFNG 1 9
## 20 IL1B 1 9
## invivo SYMBOL value
## 1 Carcinogenicity AHR 1
## 2 Neurotoxicity AHR 1
## 3 Nephrotoxicity AHR 1
## 7 Carcinogenicity FASLG 1
## 8 Neurotoxicity FASLG 1
## 13 Carcinogenicity BCL2 1
## 17 Neurotoxicity BCL2 1
## 18 Carcinogenicity BRCA1 1
## 22 Neurotoxicity BRCA1 1
## 23 Carcinogenicity MAPK14 1
## 24 Nephrotoxicity MAPK14 1
## 27 Neurotoxicity MAPK14 1
## 30 Neurotoxicity ESR1 1
## 33 Carcinogenicity ESR1 1
## 36 Nephrotoxicity GSTM1 1
## 37 Carcinogenicity GSTM1 1
## 40 Nephrotoxicity H2AX 1
## 41 Carcinogenicity H2AX 1
## 42 Neurotoxicity H2AX 1
## 44 Neurotoxicity HIF1A 1
## 48 Carcinogenicity HIF1A 1
## 50 Nephrotoxicity HMOX1 1
## 51 Neurotoxicity HMOX1 1
## 52 Carcinogenicity HMOX1 1
## 56 Neurotoxicity IFNG 1
## 59 Carcinogenicity IFNG 1
## 60 Nephrotoxicity IFNG 1
## 62 Nephrotoxicity IL1B 1
## 66 Neurotoxicity IL1B 1
#################################################
library(igraph)
##
## 载入程辑包：'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=data_edge_1, vertices=data_node, directed=FALSE)
#str(g)
#show(g)
########################################
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$Count*0.03
#E(g)$width <- (edge_1$weight*0.001)^10*300
#abs(scale(edge_1$weight))
#par(mar=c(.2,0.2,.2,.2))
#V(g)$name
#install.packages("edgebundleR")
library(edgebundleR)
tiff(filename=paste0(dir_path,"network_1.tif"),width = 20, height = 20, units = "cm",
compression = "lzw",bg = "white", res = 300, family = "serif", restoreConsole = TRUE)
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))
dev.off()
## png
## 2
#View(data_node)
#View(data_edge_1)
#install.packages("extrafont")
str(data_edge_1)
## 'data.frame': 29 obs. of 3 variables:
## $ invivo: chr " Carcinogenicity" " Neurotoxicity" " Nephrotoxicity" " Carcinogenicity" ...
## $ SYMBOL: chr "AHR" "AHR" "AHR" "FASLG" ...
## $ value : int 1 1 1 1 1 1 1 1 1 1 ...
str(data_node)
## 'data.frame': 15 obs. of 3 variables:
## $ node : chr " Carcinogenicity" " Neurotoxicity" " Nephrotoxicity" "AHR" ...
## $ number: int 1 1 1 1 1 1 1 1 1 1 ...
## $ col : int 1 2 3 9 9 9 9 9 9 9 ...
g <- graph.data.frame(data_edge_1[,1:2], directed=F,vertices=data_node)
data_node$col <- 1:nrow(data_node)
data_node$col[data_node$col >8] <- 9
clr <- as.factor(V(g)$col)
V(g)$name
## [1] " Carcinogenicity" " Neurotoxicity" " Nephrotoxicity" "AHR"
## [5] "FASLG" "BCL2" "BRCA1" "MAPK14"
## [9] "ESR1" "GSTM1" "H2AX" "HIF1A"
## [13] "HMOX1" "IFNG" "IL1B"
levels(clr) <- c(categorical_pal(8),"dodgerblue")
V(g)$color <- as.character(clr)
P1 <- edgebundle(g,tension = 0.5,cutoff = 0.1,padding = 100,fontsize = 11)
P1
saveEdgebundle(P1, "network_12.html", selfcontained = TRUE)
#?edgebundle
#getwd()
#setwd("C:/Users/liyix/OneDrive/Desktop/")
categorical_pal(8)
## [1] "#E69F00" "#56B4E9" "#009E73" "#F0E442" "#0072B2" "#D55E00" "#CC79A7"
## [8] "#999999"