誤差バーはarrowsを使用して描画した。領域はrectで描画し、densityで描画タイプを指定できる。
論文作成時のRでのグラフ描画例をいくつか挙げる。マウスで簡単に書けないのが欠点である。
cls <- function(){ while(dev.cur() > 1) {dev.off()} }
cls()
tp <- read.table("r2-20150611.csv", sep=",", header=T)
par(pin=c(7, 4))
par(mai=c(1,1,0.5,0.5)) $ BLUR
par(ps=14)
plot(0,0,type="n",xlim=range(1:170),ylim=range(-10:170),xlab="Time [min]",ylab="OCR [%]")
lines(tp[,"TIME"], tp[,"Control"], lwd=2, lty=1)
points(tp[,"TIME"], tp[,"Control"], lwd=1, pch=15, cex=1.5)
arrows(tp[,"TIME"], tp[,"Control"] + tp[,"Cdev"], tp[,"TIME"], tp[,"Control"] - tp[,"Cdev"], angle = 90, length = 0.1, lwd=2)
arrows(tp[,"TIME"], tp[,"Control"] - tp[,"Cdev"], tp[,"TIME"], tp[,"Control"] + tp[,"Cdev"], angle = 90, length = 0.1, lwd=2)
lines(c(28,28), c(-10,165), lwd=1, lty=1, )
lines(c(64,64), c(-10,165), lwd=1, lty=1, )
lines(c(99,99), c(-10,165), lwd=1, lty=1, )
lines(c(134,134), c(-10,165), lwd=1, lty=1, )
rect(28, 32, 64,100, col="blue", density=4)
text(35, 65, "ATP\nProduction", pos=4, cex=0.8, offset=0.1, col="blue", fg="white", font=2)
rect(28, 13, 64, 32, col="purple", density=4)
text(33, 21, "Proton Leak", pos=4, cex=0.8, offset=0.1, col="purple", font=2)
rect(0, 13, 28, 100, col="steelblue2", density=4)
text(0, 52, " Basal\n Respiration", pos=4, cex=0.8, offset=0.1, col="steelblue2", font=2)
rect(64, 13, 99, 152, col="red", density=4)
text(70, 80, "Maximal\nRespiration", pos=4, cex=0.8, offset=0.1, col="red", font=2)
lines(c(0,168), c(13,13), lwd=1.5, lty=1, col="green3")
rect(0,0, 168,13, col="green", density=4)
text(50, 6, "Non-mitochondrial Respiration", pos=4, cex=0.8, offset=0.1, col="green3", font=2)
lines(c(99,109), c(152,152), lty=2)
lines(c(64,109), c(100,100), lty=2)
arrows(105, 100, 105, 152, code=3, length=0.1)
text(107, 122, "Spare\nCapacity", pos=4, cex=0.8, offset=0.1, col="black", font=2)
text(28, -10, "Oligomycin", pos=4, cex=0.8, offset=0.1)
text(64, -10, "FCCP", pos=4, cex=0.8, offset=0.1)
text(99, -10, "Antimycin A", pos=4, cex=0.8, offset=0.1)
text(134,-10, "Rotenone", pos=4, cex=0.8, offset=0.1)
dev.copy2eps(device=postscript, file="r2-XF24_SF1b.eps", width=8, height=5, family="Helvetica")
cls()
cls <- function(){ while(dev.cur() > 1) {dev.off()} }
cls()
tp <- read.table("r2-XF24_1.csv", sep=",", header=T)
par(pin=c(7, 4))
par(mai=c(1,1,0.5,0.5)) $ BLUR
par(ps=16)
plot(0,0,type="n",xlim=range(1:170),ylim=range(0:200),xlab="Time [min]",ylab="OCR [%]")
lines(tp[,"TIME"], tp[,"Control"], lwd=2, lty=1, col="lightskyblue")
lines(tp[,"TIME"], tp[,"H0.1mM"], lwd=2, lty=2, col="royalblue1")
lines(tp[,"TIME"], tp[,"H0.3mM"], lwd=2, lty=3, col="slateblue3")
lines(tp[,"TIME"], tp[,"H1mM"], lwd=2, lty=4, col="orchid")
points(tp[,"TIME"], tp[,"Control"], lwd=1, pch=15, cex=1.5, col="lightskyblue")
points(tp[,"TIME"], tp[,"H0.1mM"], lwd=1, pch=16, cex=1.5, col="royalblue1")
points(tp[,"TIME"], tp[,"H0.3mM"], lwd=1, pch=17, cex=1.5, col="slateblue3")
points(tp[,"TIME"], tp[,"H1mM"], lwd=1, pch=18, cex=1.5, col="orchid")
arrows(tp[,"TIME"], tp[,"Control"] + tp[,"Cdev"], tp[,"TIME"], tp[,"Control"] - tp[,"Cdev"], angle = 90, length = 0.1, lwd=2, col="lightskyblue")
arrows(tp[,"TIME"], tp[,"Control"] - tp[,"Cdev"], tp[,"TIME"], tp[,"Control"] + tp[,"Cdev"], angle = 90, length = 0.1, lwd=2, col="lightskyblue")
arrows(tp[,"TIME"], tp[,"H0.1mM"] + tp[,"H0.1mMdev"], tp[,"TIME"], tp[,"H0.1mM"] - tp[,"H0.1mMdev"], angle = 90, length = 0.1, lwd=2, col="royalblue1")
arrows(tp[,"TIME"], tp[,"H0.1mM"] - tp[,"H0.1mMdev"], tp[,"TIME"], tp[,"H0.1mM"] + tp[,"H0.1mMdev"], angle = 90, length = 0.1, lwd=2, col="royalblue1")
arrows(tp[,"TIME"], tp[,"H0.3mM"] + tp[,"H0.3mMdev"], tp[,"TIME"], tp[,"H0.3mM"] - tp[,"H0.3mMdev"], angle = 90, length = 0.1, lwd=2, col="slateblue3")
arrows(tp[,"TIME"], tp[,"H0.3mM"] - tp[,"H0.3mMdev"], tp[,"TIME"], tp[,"H0.3mM"] + tp[,"H0.3mMdev"], angle = 90, length = 0.1, lwd=2, col="slateblue3")
arrows(tp[,"TIME"], tp[,"H1mM"] + tp[,"H1mMdev"], tp[,"TIME"], tp[,"H1mM"] - tp[,"H1mMdev"], angle = 90, length = 0.1, lwd=2, col="orchid")
arrows(tp[,"TIME"], tp[,"H1mM"] - tp[,"H1mMdev"], tp[,"TIME"], tp[,"H1mM"] + tp[,"H1mMdev"], angle = 90, length = 0.1, lwd=2, col="orchid")
lines(c(28,28), c(0,200), lwd=1, lty=1, )
lines(c(64,64), c(0,200), lwd=1, lty=1, )
lines(c(99,99), c(0,200), lwd=1, lty=1, )
lines(c(134,134), c(0,200), lwd=1, lty=1, )
text(28,0, "Oligomycin", pos=4, cex=0.8, offset=0.1)
text(64,0, "FCCP", pos=4, cex=0.8, offset=0.1)
text(99,0, "Antimycin", pos=4, cex=0.8, offset=0.1)
text(134,0, "Rotenone", pos=4, cex=0.8, offset=0.1)
leg <- c(" Control",
expression(paste(" ", paste(paste(H[2],O[2])," 0.1 mM 1hr"))),
expression(paste(" ", paste(paste(H[2],O[2])," 0.3 mM 1hr"))),
expression(paste(" ", paste(paste(H[2],O[2])," 1.0 mM 1hr"))))
legend("topright", legend = leg, pch = c(15,16,17,18), lty = c(1,2,3,4), bg="white", y.intersp=2, xjust=1, col=c("lightskyblue","royalblue1","slateblue3","orchid"))
dev.copy2eps(device=postscript, file="r2-XF24_F5a_col.eps", width=8, height=5, family="Helvetica")
cls()
cls <- function(){ while(dev.cur() > 1) {dev.off()} }
cls()
par(pin=c(4, 4))
par(mai=c(1,1,0.5,0.5)) $ BLUR
par(ps=15)
leg2 <- c(" Control", "0.1 mM", "0.3 mM", "1.0 mM")
jc1 <- c(1.0079774, 0.957234643, 0.931015671, 0.886195603)
jc1_dev <- c(0.021088766, 0.01139586, 0.014554344, 0.024889494)
C <- barplot(jc1, ylim=c(0.8,1.099), ylab="RFU(590nm)/RFU(535nm)", space=1, col=c("lightskyblue","royalblue1","slateblue3","orchid"),names.arg=leg2, xpd=F)
arrows(C, jc1 - jc1_dev, C, jc1 + jc1_dev, angle = 90, length = 0.1)
arrows(C, jc1 + jc1_dev, C, jc1 - jc1_dev, angle = 90, length = 0.1)
box("plot",lty=1)
drawbraces <- function(x1,x2,y) {
segments(x1,y, x2,y)
segments(x1,y, x1,y-0.005)
segments(x2,y, x2,y-0.005)
}
drawbraces(1.5,3.5,1.05)
drawbraces(1.5,5.5,1.065)
drawbraces(1.5,7.5,1.08)
text(2.5,1.051, "*", pos=4, cex=0.9, offset=0)
text(3.5,1.066, "*", pos=4, cex=0.9, offset=0)
text(4.5,1.081, "*", pos=4, cex=0.9, offset=0)
dev.copy2eps(device=postscript, file="r2-XF24_F4_color.eps", width=5, height=5, family="Helvetica")
cls()
描画方向をひっくり返すのはylimでパラメータを逆にすれば良い。par(new=T)で重ね描きすれば両方向のグラフができる。 軸の描画自体はaxisであるが、パラメータをpar()から取得したりするのは知らないとやや面倒である。
cls <- function(){ while(dev.cur() > 1) {dev.off()} }
cls()
tp <- read.table("r2-20160406_H1_MT_combined.csv", sep=",", header=T)
str(tp)
par(pin=c(4, 4))
par(mai=c(1,1,0.5,0.5)) $ BLUR
par(ps=15)
c1 <- subset(tp,TYPE=="CONT")[["Branches"]]
c2 <- subset(tp,TYPE=="HYD" )[["Branches"]]
plot.new()
plot.window(ylim = c(-2, 2), xlim = c(0, 5))
par(new = TRUE)
hist(log(c1+1),probability=TRUE,xlim=c(0,5),ylim=c(-2,2),col="lightskyblue",axes = FALSE, xlab = "", ylab = "", main = "",breaks=8)
par(new = TRUE)
hist(log(c2+1),probability=TRUE,xlim=c(0,5),ylim=c(2,-2),col="orchid",axes = FALSE, xlab = "ln(Branch Count+1)", ylab = "Density", main = "",breaks=5)
axis(side = 2, at = pretty(par()$usr[3:4]), labels = abs(pretty(par()$usr[3:4])))
axis(side = 1)
leg <- c(" Control",
expression(paste(" ", paste(paste(H[2],O[2])," 0.1mM 1hr "))))
legend("topright", legend = leg, pch = c(15,15), bg="white", y.intersp=2, xjust=1, col=c("lightskyblue","orchid"))
dev.copy2eps(device=postscript, file="r2-XF24_F3_branch.eps", width=5, height=5, family="Helvetica")
cls()
Your supervisor is thinking about you.
I think, to most people, scripting is a lot like obscenity. I can't define it,
but I'll know it when I see it. Here are some common memes floating around:
<<<
Simple language
"Everything is a string"
Rapid prototyping
Glue language
Process control
Compact/concise
Worse-is-better
Domain specific
"Batteries included"
>>>
...I don't see any real center here, at least in terms of technology. If I had
to pick one metaphor, it'd be easy onramps. And a slow lane. Maybe even with
some optional fast lanes.
-- Larry Wall
-- "Programming is Hard, Let's Go Scripting" ( http://www.perl.com/pub/a/2007/12/06/soto-11.html )