Plot

Base

• R base plotting without wrappers

math formula

比如

expression(R[group("", list(hat(F),F),"")]^2)

参考

1. Mathematical Annotation in R

pure figure without axis

Suppose I want to draw the following figure with R,

At first, I try to use xaxt option to remove the axis, but the box still remains, just same as the one question in the StackOverflow, and I found a possible solution, directly use

plot.new()

All is well before I tried to add the text $\rho$, if I use

text(0.8, 0, expression(rho), cex = 2)

it is OK, but it is exactly on the axis, not proper, but when I tried smaller $y$-coordinate, such as -0.1, the text cannot appear, which seems out of the figure. I have tried par() parameters, such as mar, but does not work.

Then I have no idea, and do not know how to google it. And even though I want to post an issue in the StackOverflow. But a random reference give me ideas, in which the example saves me,

> plot.new()
> plot.window(xlim=c(0,1), ylim=c(5,10))
> abline(a=6, b=3)
> axis(1)
> axis(2)
> title(main="The Overall Title")
> title(xlab="An x-axis label")
> title(ylab="A y-axis label")
> box()

Then I realized that I should add

plot.window(xlim = c(0, 1), ylim = c(-0.1, 0.9))

smooth curve

x <- 1:10
y <- c(2,4,6,8,7,12,14,16,18,20)
lo <- loess(y~x)
plot(x,y)
lines(predict(lo), col='red', lwd=2)

参考How to fit a smooth curve to my data in R?

margin

有时通过 par(mfrow=c(2,1)) 画图时间距过大，这可以通过 mar 来调节，注意到

• mar 调节单张图的 margin
• oma 调节整张图外部的 margin

参考 how to reduce space gap between multiple graphs in R

比如，B spline in R, C++ and Python

custom panels in pairs

问题来自R语言绘图？ - 知乎

my.lower <- function(x,y,...){
  points(x, y)
  lines(lowess(x, y), col = "red", lwd=2)
}

my.upper <- function(x, y, ...){
  cor.val = round(cor(x,y), digits = 3)
  if (abs(cor.val) > 0.5){
    text(mean(x), mean(y), cor.val, cex = 3)
    text(sort(x)[length(x)*0.8], max(y), '***', cex = 4, col = "red")
  } else
  {
    text(mean(x), mean(y), cor.val, cex = 1)
  }
}

pairs(iris[1:4], lower.panel =my.lower, upper.panel = my.upper)

参考 Different data in upper and lower panel of scatterplot matrix

lattice

The package can easily generate trellis graphs. A trellis graph displays the distribution of a variable or the relationship between variables, separately for each level of one or more other variables.

A thorough tutorial refers to Reproduce Figures with Lattice – ESL CN

ggplot

• https://ggplot2-book.org/

multiple density plots

参考使用ggplot2同时绘制多个密度图

plots <- NULL
for(i in colnames(train)){ 
    plots[[i]] <- ggplot(train) + 
    geom_density(aes_string(x = i, fill = 'is_black'), alpha = 0.5, show.legend = F) + 
    xlab("") + 
    ylab(""); 
}
plot_grid(plotlist = plots)

see also: Continuously add lines to ggplot with for loop

density of Weibull

adapted from ggplot2绘制概率密度图

Take the Weibull distribution as an example,

$$f(x) = \begin{cases} \frac k\lambda \left(\frac x\lambda\right)^{k-1}e^{-(x/\lambda)^k} & x\ge 0\\ 0 & x < 0 \end{cases}$$

where $\lambda > 0$ is the scale parameter, and $k > 0$ is the shape parameter. And

• if $k=1$, it becomes to the exponential distribution
• if $k=2$, it becomes to the Rayleigh distribution.

dweibullrweibull + histogramrweibull + densityrweibull + line

d <- seq(0, 5, length.out=10000)
y <- dweibull(d, shape=5, scale=1, log = FALSE)
df <- data.frame(x=d,y)
ggplot(df, aes(x=d, y=y)) + 
    geom_line(col = "orange") + 
    ggtitle("Density of Weibull distribution")

h = rweibull(10000, shape=5, scale=1)
ggplot(NULL, aes(x=h)) + 
    geom_histogram(binwidth=0.01, fill="white", col="red") + 
    ggtitle("Histogram of Weibull distribution")

ggplot(NULL, aes(x=h)) + geom_density(col = "green")

ggplot(NULL, aes(x=h)) + geom_line(stat = "density", col = "red")

A minor difference is that here is a horizontal line in the above estimated density.

Also refer to Plotting distributions (ggplot2)

legend setup

参考Legends (ggplot2)

默认情形

library(ggplot2)
bp <- ggplot(data=PlantGrowth, aes(x=group, y=weight, fill=group)) + geom_boxplot()
bp

自定义图例的顺序

首先移除掉默认图例，有三种方式实现：

# Remove legend for a particular aesthetic (fill)
bp + guides(fill=FALSE)

# It can also be done when specifying the scale
bp + scale_fill_discrete(guide=FALSE)

# This removes all legends
bp + theme(legend.position="none")

再改变默认顺序

bp + scale_fill_discrete(breaks=c("trt1","ctrl","trt2"))

颠倒图例的顺序

# These two methods are equivalent:
bp + guides(fill = guide_legend(reverse=TRUE))
bp + scale_fill_discrete(guide = guide_legend(reverse=TRUE))

# You can also modify the scale directly:
bp + scale_fill_discrete(breaks = rev(levels(PlantGrowth$group)))

隐藏图例标题

# Remove title for fill legend
bp + guides(fill=guide_legend(title=NULL))

# Remove title for all legends
bp + theme(legend.title=element_blank())

自定义图例的标题及名称

两种方式，一种 另一种修改数据集

图例的整体形状

# Title appearance
bp + theme(legend.title = element_text(colour="blue", size=16, face="bold"))

# Label appearance
bp + theme(legend.text = element_text(colour="blue", size = 16, face = "bold"))

图例盒子

bp + theme(legend.background = element_rect())
bp + theme(legend.background = element_rect(fill="gray90", size=.5, linetype="dotted"))

图例位置

bp + theme(legend.position="top")

# Position legend in graph, where x,y is 0,0 (bottom left) to 1,1 (top right)
bp + theme(legend.position=c(.5, .5))

# Set the "anchoring point" of the legend (bottom-left is 0,0; top-right is 1,1)
# Put bottom-left corner of legend box in bottom-left corner of graph
bp + theme(legend.justification=c(0,0), legend.position=c(0,0))

# Put bottom-right corner of legend box in bottom-right corner of graph
bp + theme(legend.justification=c(1,0), legend.position=c(1,0))

隐藏图例的slashes

# No outline
ggplot(data=PlantGrowth, aes(x=group, fill=group)) +
    geom_bar()

# Add outline, but slashes appear in legend
ggplot(data=PlantGrowth, aes(x=group, fill=group)) +
    geom_bar(colour="black")

# A hack to hide the slashes: first graph the bars with no outline and add the legend,
# then graph the bars again with outline, but with a blank legend.
ggplot(data=PlantGrowth, aes(x=group, fill=group)) +
    geom_bar() +
    geom_bar(colour="black", show.legend=FALSE)

坐标轴标签字体大小

参考Size of labels for x-axis and y-axis ggplot in R

多张图片

par(mfrow=c(1,2))不起作用，要用到 gridExtra 包，如

library(gridExtra)
plot1 <- qplot(1)
plot2 <- qplot(1)
grid.arrange(plot1, plot2, ncol=2)

参考Side-by-side plots with ggplot2

绘制地图

参考

1. Making Maps with R

scale_fill_manual 和 scale_color_manual

更改颜色命令为

scale_fill_manual(values = c("red", "blue"))

save

NOT png()...dev.off(), use

ggsave("sth.eps",device="eps", width=9)

aes_string vs aes

在重复绘图时，似乎是作用域的缘故，有时 aes 只能保留最后一个，此时需要用 aes_string.

参考 Question: Continuously add lines to ggplot with for loop