java改图软件_java版本GSEA软件的ES score图片的修改

setwd('data')

Obs.RES=read.table('Obs.RES.txt')

Obs.RES=t(Obs.RES) ## 每个基因在每个gene set里面的running ES score，一个矩阵

Obs.indicator=read.table('Obs.indicator.txt')

Obs.indicator=t(Obs.indicator) ## 每个基因是否属于每个gene set，一个0/1矩阵

obs.s2n=read.table('obs.s2n.txt')[,1]  ## 每个基因的signal 2 noise值，已经Z-score化，而且排好序了。

size.G=read.table('size.G.txt')[,1]  ## 每个gene set的基因数量，在图中需要显示

gs.names=read.table('gs.names.txt')[,1] ## 每个gene set的名字，在图中需要显示

Obs.arg.ES=read.table('Obs.arg.ES.txt')[,1]## 每个gene set的最大ES score出现在排序基因的位置

Obs.ES.index=read.table('Obs.ES.index.txt')[,1]## 这个用不着的，我也忘记是什么了

Obs.ES=read.table('Obs.ES.txt')[,1]  ##每个gene set的最大ES score是多少，如果是正值，用红色表示富集在case组，如果是负值，用蓝色，表示富集在control组。

plot_ES_score

for (i in 1:Ng) {

png(paste0('number_',gs.names[i],'.png'))

ind

min.RES

max.RES

if (max.RES < 0.3) max.RES

if (min.RES > -0.3) min.RES

delta

min.plot

max.plot

max.corr

min.corr

Obs.correl.vector.norm

zero.corr.line

col 0, 2, 4)

# Running enrichment plot

sub.string

main.string

plot(ind, Obs.RES[i,], main = main.string, sub = sub.string, xlab = "Gene List Index", ylab = "Running Enrichment Score (RES)", xlim=c(1, N), ylim=c(min.plot, max.plot), type = "l", lwd = 2, cex = 1, col = col)

for (j in seq(1, N, 20)) {

lines(c(j, j), c(zero.corr.line, Obs.correl.vector.norm[j]), lwd = 1, cex = 1, col = colors()[12]) # shading of correlation plot

}

lines(c(1, N), c(0, 0), lwd = 1, lty = 2, cex = 1, col = 1) # zero RES line

lines(c(Obs.arg.ES[i], Obs.arg.ES[i]), c(min.plot, max.plot), lwd = 1, lty = 3, cex = 1, col = col) # max enrichment vertical line

for (j in 1:N) {

if (Obs.indicator[i, j] == 1) {

lines(c(j, j), c(min.plot + 1.25*delta, min.plot + 1.75*delta), lwd = 1, lty = 1, cex = 1, col = 1) # enrichment tags

}

}

lines(ind, Obs.correl.vector.norm, type = "l", lwd = 1, cex = 1, col = 1)

lines(c(1, N), c(zero.corr.line, zero.corr.line), lwd = 1, lty = 1, cex = 1, col = 1) # zero correlation horizontal line

temp

arg.correl

lines(c(arg.correl, arg.correl), c(min.plot, max.plot), lwd = 1, lty = 3, cex = 1, col = 3) # zero crossing correlation vertical line

leg.txt

text(x=1, y=min.plot, adj = c(0, 0), labels=leg.txt, cex = 1.0)

leg.txt

text(x=N, y=min.plot, adj = c(1, 0), labels=leg.txt, cex = 1.0)

adjx 0, 0, 1)

leg.txt

text(x=Obs.arg.ES[i], y=min.plot + 1.8*delta, adj = c(adjx, 0), labels=leg.txt, cex = 1.0)

leg.txt

text(x=arg.correl, y=min.plot + 1.95*delta, adj = c(adjx, 0), labels=leg.txt, cex = 1.0)

dev.off()

}

}