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()
<ubajas> Technically, my first language was Turbo Pascal, but I
started over with Perl 10 years later (not having
programmed in the meantime). I'm obviously damaged goods.
<iank> ubajas: heh, I read that as "I started with (perl 10)
(years later)" instead of "I started with perl (10 years
later)" :)
<rindolf> Perl 10!
<rindolf> Perl for the Fourth Millenium.
<jagerman> I thought Perl 6 was supposed to be timeless
<ubajas> iank: Maybe I should have added a comma. :-]
<jagerman> Perl ���
<iank> perl6 has existed since the beginning of time, or at least
it will have existed since then once $Larry finds a time
machine.
<simcop2387> iank: i'm sorry but larry is the prophet i am the
messanger! i will be the one to take it back!
<iank> WHAT.
<simcop2387> iank: its MY TIME MACHINE!
* iank smacks simcop2387 around
<jagerman> iank: So it'll be like that Star Trek episode, where they
say that the development of computers are caused by time
travel from the future?
<jagerman> Except that they were too stupid (like most Voyager
writers) to get their facts right, and thought computers
started in the 70s
-- The Messiah of Perl
-- #perl, Freenode
What happened to Christopher Michael Pilato?
Is he gone?
Is he gone for good?
Is he gone for better?
Is he gone for best?
Is he gone forever?
Will he return?
Who is Christopher Michael Pilato, anyway?
Shlomi Fish
-- Shlomi Fish
-- Adapted from an IRC Monologue