R语言基础（二）：绘图初步
需要安装的包：
install.packages(c("RColorBrewer","lattice","survival","ggplot2","Formula","mice"))R语言的绘图系统：
- 第一代绘图系统
- 基于
lattic的系统 - 基于
ggplot2的绘图系统
绘图初步
绘图例子
par(ask=FALSE)
par(pin=c(5, 3))
temp <- par(pin <- c(4.2,2.3))
par(temp)## named list()#par(ask=TRUE)
#win.graph(width=4.875, height=2.5,pointsize=8)
opar <- par(no.readonly=TRUE) # make a copy of current settings
#win.graph(width=4.875, height=2.5,pointsize=8)
attach(mtcars) # be sure to execute this line
plot(wt, mpg)
abline(lm(mpg~wt))
title("Regression of MPG on Weight")
detach(mtcars)保存到文件
使用pdf() 函数：
pdf("mygraph.pdf")
attach(mtcars)
plot(wt, mpg)
abline(lm(mpg~wt))
title("Regression of MPG on Weight")
detach(mtcars)
dev.off()## png
## 2除了pdf()，还可以使用函数win.metafile()、png()、jpeg()、bmp()、tiff()、xfig() 和postscript()将图形保存为其他格式。
对数据集绘图
例子
drug example
# Input data for drug example
dose <- c(20, 30, 40, 45, 60)
drugA <- c(16, 20, 27, 40, 60)
drugB <- c(15, 18, 25, 31, 40)#win.graph(width=4.875, height=2.5,pointsize=8)
plot(dose, drugA, type="b")
图形参数
通过函数par()来指定绘图选项
?par()修改参数
使用实心三角而不是空心圆圈作为点的符号，并且想用虚线代替实线连接这些点:
opar <- par(no.readonly=TRUE) # make a copy of current settings
par(lty=2, pch=17) # change line type and symbol
plot(dose, drugA, type="b") # generate a plot
par(opar) # restore the original settings 
符号和线条类型的参数
符号和线条类型的参数
符号和线条类型的参数
plot(dose, drugA, type="b", lty=3, lwd=3, pch=15, cex=2)
修改颜色
指定颜色的参数
# choosing colors
library(RColorBrewer)
n <- 7
mycolors <- brewer.pal(n, "Set1")
barplot(rep(1,n), col=mycolors)
颜色集合的选择可以使用包RColorBrewer
n <- 10
mycolors <- rainbow(n)
pie(rep(1, n), labels=mycolors, col=mycolors)
mygrays <- gray(0:n/n)
pie(rep(1, n), labels=mygrays, col=mygrays)
使用col()改变颜色
# - Using graphical parameters to control graph appearance
opar <- par(no.readonly=TRUE)
par(pin=c(2, 3))
par(lwd=2, cex=1.5)
par(cex.axis=.75, font.axis=3)
#win.graph(width=4.875, height=2.5,pointsize=8)
plot(dose, drugA, type="b", pch=19, lty=2, col="red")
plot(dose, drugB, type="b", pch=23, lty=6, col="blue", bg="green")
par(opar) 添加文本、自定义坐标轴和图例
# Adding text, lines, and symbols
#win.graph(width=4.875, height=2.5,pointsize=8)
plot(dose, drugA, type="b",
col="red", lty=2, pch=2, lwd=2,
main="Clinical Trials for Drug A",
sub="This is hypothetical data",
xlab="Dosage", ylab="Drug Response",
xlim=c(0, 60), ylim=c(0, 70))
# Listing 3.2 - An Example of Custom Axes
x <- c(1:10)
y <- x
z <- 10/x
opar <- par(no.readonly=TRUE)
par(mar=c(5, 4, 4, 8) + 0.1)
plot(x, y, type="b",
pch=21, col="red",
yaxt="n", lty=3, ann=FALSE)
lines(x, z, type="b", pch=22, col="blue", lty=2)
axis(2, at=x, labels=x, col.axis="red", las=2)
axis(4, at=z, labels=round(z, digits=2),
col.axis="blue", las=2, cex.axis=0.7, tck=-.01)
mtext("y=1/x", side=4, line=3, cex.lab=1, las=2, col="blue")
title("An Example of Creative Axes",
xlab="X values",
ylab="Y=X")
par(opar)# Listing 3.3 - Comparing Drug A and Drug B response by dose
dose <- c(20, 30, 40, 45, 60)
drugA <- c(16, 20, 27, 40, 60)
drugB <- c(15, 18, 25, 31, 40)
opar <- par(no.readonly=TRUE)
par(lwd=2, cex=1.5, font.lab=2)
#win.graph(width=4.875, height=2.5,pointsize=8)
plot(dose, drugA, type="b",
pch=15, lty=1, col="red", ylim=c(0, 60),
main="Drug A vs. Drug B",
xlab="Drug Dosage", ylab="Drug Response")
lines(dose, drugB, type="b",
pch=17, lty=2, col="blue")
abline(h=c(30), lwd=1.5, lty=2, col="gray")
library(Hmisc)## Loading required package: lattice## Loading required package: survival## Loading required package: Formula## Loading required package: ggplot2##
## Attaching package: 'Hmisc'## The following objects are masked from 'package:base':
##
## format.pval, round.POSIXt, trunc.POSIXt, unitsminor.tick(nx=3, ny=3, tick.ratio=0.5)
legend("topleft", inset=.05, title="Drug Type", c("A","B"), lty=c(1, 2), pch=c(15, 17), col=c("red", "blue"))
par(opar)# Example of labeling points
attach(mtcars)## The following object is masked from package:ggplot2:
##
## mpg#win.graph(width=8.875, height=8.5,pointsize=8)
plot(wt, mpg,
main="Mileage vs. Car Weight",
xlab="Weight", ylab="Mileage",
pch=18, col="blue")
text(wt, mpg,
row.names(mtcars),
cex=0.6, pos=4, col="red")
detach(mtcars)# View font families
opar <- par(no.readonly=TRUE)
par(cex=1.5)
#win.graph(width=4.875, height=2.5,pointsize=8)
plot(1:7,1:7,type="n")
text(3,3,"Example of default text")
text(4,4,family="mono","Example of mono-spaced text")
text(5,5,family="serif","Example of serif text")
par(opar)# Combining graphs
attach(mtcars)## The following object is masked from package:ggplot2:
##
## mpgopar <- par(no.readonly=TRUE)
par(mfrow=c(2,2))
par(ask=FALSE)
plot(wt,mpg, main="Scatterplot of wt vs. mpg")
plot(wt,disp, main="Scatterplot of wt vs. disp")
hist(wt, main="Histogram of wt")
boxplot(wt, main="Boxplot of wt")
par(opar)
detach(mtcars)attach(mtcars)## The following object is masked from package:ggplot2:
##
## mpgopar <- par(no.readonly=TRUE)
#win.graph(width=4.875, height=2.5,pointsize=8)
par(mfrow=c(3,1))
hist(wt)
hist(mpg)
hist(disp)
par(opar)
detach(mtcars)attach(mtcars)## The following object is masked from package:ggplot2:
##
## mpglayout(matrix(c(1,1,2,3), 2, 2, byrow = TRUE))
hist(wt)
hist(mpg)
hist(disp)
detach(mtcars)attach(mtcars)## The following object is masked from package:ggplot2:
##
## mpglayout(matrix(c(1, 1, 2, 3), 2, 2, byrow = TRUE),
widths=c(3, 1), heights=c(1, 2))
hist(wt)
hist(mpg)
hist(disp)
detach(mtcars)# Listing 3.4 - Fine placement of figures in a graph
opar <- par(no.readonly=TRUE)
par(fig=c(0, 0.8, 0, 0.8))
plot(mtcars$mpg, mtcars$wt,
xlab="Miles Per Gallon",
ylab="Car Weight")
par(fig=c(0, 0.8, 0.55, 1), new=TRUE)
boxplot(mtcars$mpg, horizontal=TRUE, axes=FALSE)
par(fig=c(0.65, 1, 0, 0.8), new=TRUE)
boxplot(mtcars$wt, axes=FALSE)
mtext("Enhanced Scatterplot", side=3, outer=TRUE, line=-3)
par(opar)绘图实例
实例（一）
cit <- c( 2010, 37, 182, NA,
2009, 36, 129, NA,
2008, 27, 111, NA,
2007, 35, 136, NA,
2006, 18, 80, NA,
2005, 20, 76, NA,
2004, 6, 56, NA,
2003, 17, 42, NA,
2002, 14, 40, NA,
2001, 13, 36, 57,
2000, 8, 21, 33,
1999, 6, 25, 47,
1998, 6, 13, 22,
1997, 6, 18, 29,
1996, 4, 12, 28,
1995, 3, 5, 20,
1994, 2, 5, 34,
1993, 2, 6, 15,
1991, 2, 4, 19,
1990, 1, 2, 15,
1989, NA, NA, 11,
1988, 1, NA, 13,
1987, NA, NA, 10,
1986, NA, NA, 5,
1985, NA, NA, 1,
1984, NA, NA, 2,
1983, NA, NA, 5,
1982, NA, NA, 2,
1981, NA, NA, 1,
1980, NA, NA, 5,
1979, NA, NA, 2,
1978, NA, NA, 1,
1977, NA, NA, 2)
cit <- matrix(cit, nr=2010-1977, nc=4, byrow=TRUE)
cit <- as.data.frame(cit)
names(cit) <- c("Year","Title","Abstract","All")
par(mfrow=c(1,1))
par(cex=0.7, lwd=0.5)
plot(x=cit$Year, y=cit$Abstract, type="o",log="y",
xlim=c(1975,2010),ylim=c(1,200),
ylab="Number of publications (log)", xlab="Year", pch=2,
axes=FALSE)
axis(1, lwd=par("lwd"))
axis(2, lwd=par("lwd"), las=1)
# box(lwd=0.5)
lines(x=cit$Year, y=cit$Title, pch=15, type="o")
lines(x=cit$Year, y=cit$All, pch=16, type="o")
legend(x=1975,y=200,legend=c("early publications",
"'multiple imputation' in abstract",
"'multiple imputation' in title"),
pch=c(16,2,15), bty="n")
实例（二）
library("MASS")
library("mice")## Loading required package: Rcpp## mice 2.25 2015-11-09library("lattice")
logistic <- function(x) exp(x)/(1+exp(x))
set.seed(80122)
n <- 300
y <- mvrnorm(n=n,mu=c(0,0),Sigma=matrix(c(1,0.5,0.5,1),nrow=2))
y1 <- y[,1]
y2 <- y[,2]
r2.mcar <- 1-rbinom(n, 1, 0.5)
r2.mar <- 1-rbinom(n, 1, logistic(y1))
r2.mnar <- 1-rbinom(n, 1, logistic(y2))
### Figure 2.2
y3 <- rbind(y,y,y)
r2 <- c(r2.mcar,r2.mar,r2.mnar)
r2 <- factor(r2, labels=c("Ymis","Yobs"))
typ <- factor(rep(3:1,each=n),labels=c("MNAR","MAR","MCAR"))
d <- data.frame(y1=y3[,1],y2=y3[,2],r2=r2,typ=typ)
trellis.par.set(box.rectangle=list(col=c(mdc(2),mdc(1)),lwd=1.2))
trellis.par.set(box.umbrella=list(col=c(mdc(2),mdc(1)),lwd=1.2))
trellis.par.set(plot.symbol=list(col=mdc(3),lwd=1))
tp <- bwplot(r2~y2|typ, data=d,
horizontal=TRUE, layout=c(1,3),
xlab=expression(Y^2),
col=c(mdc(2),mdc(1)),strip=FALSE, xlim=c(-3,3),
strip.left = strip.custom(bg="grey95"))
print(tp)
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