jbnara

source("https://bioconductor.org/biocLite.R")

biocLite("STRINGdb")

library(STRINGdb)

library(igraph)

g <- read.graph("karate.net", format="pajek")

d <- get.diameter(g)

L <- graph(n=9,c(1,4,2,4,3,4,4,5,5,6,6,7,7,8,8,9),directed=F)

plot(L, layout=layout.fruchterman.reingold, edge.arrow.mode="-", edge.width=2, vertex.label.cex=1.2)

g <- graph.empty (5, directed = FALSE)

new_edges <- c(1,3, 1,5, 2,5, 4,5)

g <- add.edges(g, new_edges)

plot(g)

library(igraph)

dat = as.matrix(read.table('/Users/lsy/Downloads/string_interactions.tsv',sep='\t',header = FALSE))

#dat = rbind(dat,c("BCAM","","0","0","9606.ENSP00000363071","0","0","0","0","0","0","0","0.0","0","0"))

edges = as.vector(t(dat[,1:2]))

g<-graph(edges, n=max(edges), isolates=c("BCAM"))

get.edgelist(g)

plot(g, layout = layout.fruchterman.reingold, vertex.label=V(g)$number,edge.arrow.size=0.5)

library(igraph)

dat = as.matrix(read.table('/Users/lsy/Downloads/string_interactions.tsv',sep='\t',header = FALSE))

edges = as.vector(t(dat[,1:2]))

net <- graph_from_data_frame(d=dat, vertices=unique(edges), directed=T) 

plot(net, edge.arrow.size=.4,vertex.label=NA)

as_data_frame(net, what="edges")

as_data_frame(net, what="vertices")

plot(net, vertex.shape="none", vertex.label=names(V(net)), 

  vertex.label.font=2, vertex.label.color="gray40",

  vertex.label.cex=.7, edge.color="gray85")

E(net)$color[E(net)$weight > 2] <- 'green'

plot.igraph(net,vertex.label=V(net)$name,layout=layout.fruchterman.reingold,edge.arrow.size=0.2,

            vertex.label.color="gray40",edge.color="red",vertex.shape="none"

)

E(testgraph)$color <- as.factor(edges$department)

E(g)$lty[E(g)$weight == 8] <- 1

E(g)$color[E(g)$weight == 3] <- 'green'

E(g)$lty[E(g)$weight == 3] <- 2

library(igraph)

dat = as.matrix(read.table('/Users/lsy/Downloads/string_interactions.tsv',sep='\t',header = FALSE))

edges = as.vector(t(dat[,1:2]))

g<-graph(edges, n=max(edges), isolates=c("BCAM"), directed=FALSE)

E(g)$weight = as.numeric(dat[,15])

E(g)$color <-"skyblue"

E(g)$color[which(E(g)$weight > 0.7)] ="blue"

V(g)$color <-c('red','red','yellow','red','yellow','yellow','yellow')

plot.igraph(g,layout=layout.fruchterman.reingold,

            vertex.shape="circle",vertex.color=c("#Eddfed","#Eddfed","#90A66A","#Eddfed","#C45A63","#C45A63","#C45A63")

            ,vertex.size=30,

            vertex.label=V(g)$name, vertex.label.color=V(g)$color,vertex.label.cex=1, vertex.frame.color= "white",

            edge.arrow.size=0.2,edge.color=E(g)$color,edge.label=c("","PM1689487","","","","PM27559130","",""),

            edge.label.color="black",edge.label.cex=0.7

)

g<-graph(edges, n=max(edges), isolates=c("Glioblastoma\ngene","Damaging\nnsSNV","Tolerated\nnsSNV"), directed=FALSE)

V(g)$color <-c('red','red','yellow','red','yellow','yellow','red','yellow','yellow')

plot.igraph(g,layout=layout.fruchterman.reingold,

            vertex.shape="circle",

            vertex.color=c("#Eddfed","#Eddfed","#90A66A","#Eddfed","#C45A63","#C45A63","#Eddfed","#C45A63","#90A66A")

            ,vertex.size=50,

            vertex.label=V(g)$name, vertex.label.color=V(g)$color,vertex.label.cex=1, vertex.frame.color= "white",

            edge.arrow.size=0.2,edge.color=E(g)$color,edge.label=c("","PM1689487","","","","PM27559130","",""),

            edge.label.color="black",edge.label.cex=0.7

)

de

legend("topleft", legend=c("interaction score > 0.7", "0.7 < interaction score > 0.4"), col=c("blue", "skyblue"), lty=1, cex=0.8)

sudo apt-get install tabix
sort -k1,1 -k2,2 -V -s 1_20171123_ptm_info.txt > 1.txt
bgzip 1.txt
tabix -s 1 -b 2 -e 2 1.txt.gz 

bp = barplot(table(dat[,1]),las=2,ylim = c(0,600),main="Number of experience per cell line in the L1000 data")

text(x = bp, y = table(dat[,1]), label = table(dat[,1]), pos = 3, cex = 0.8, col = "red")

bp = barplot(table(dat[,1]),las=2,ylim = c(0,600),main="Number of experience per cell line in the L1000 data")

text(x = bp, y = table(dat[,1]), label = table(dat[,1]), pos = 3, cex = 0.8, col = "red")