qplot 使用
导入所需数据格式为data.frame
data(mtcars)
df <- mtcars[, c("mpg", "cyl", "wt")]
head(df)
qplot()基本用法
qplot(x, y=NULL, data, geom="auto",
xlim = c(NA, NA), ylim =c(NA, NA))
# geom 画什么图；main 题目；xlab,ylab xy轴标签
# color 颜色；size 点大小；shape 点形状
Scatter plots 散点图
library(ggplot2)
# 基本款
qplot(mpg, wt, data=mtcars)
# 增加standard error和 smoothed line
qplot(mpg, wt, data = mtcars, geom = c("point", "smooth"))
# 分组增加smoothed line
qplot(mpg, wt, data = mtcars, color = factor(cyl),
geom=c("point", "smooth"))
image.png
boxplot violin plot
boxplot
geom="boxplot"
dotplot
geom="dotplot"
violin
geom="violin"
# Basic box plot from data frame
qplot(group, weight, data = PlantGrowth,
geom=c("boxplot"), fill = group)
# fill 填充颜色
# Dot plot
qplot(group, weight, data = PlantGrowth,
geom=c("dotplot"),
stackdir = "center", binaxis = "y",color = group, fill = group)
# Violin plot
qplot(group, weight, data = PlantGrowth,
geom=c("violin"), trim = FALSE, fill = group)
histogram density plot
qplot(Sepal.Length, data = iris, geom = "histogram", binwidth=0.1)
qplot(Sepal.Length, data = iris, geom = "density", color = Species,
main = "test", xlab = "x_test", ylab = "y_test")
ggplot2 box plot
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
# notched box plot
ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_boxplot(notch=TRUE, outlier.color = "red")
改变线颜色
三种方法
p<-ggplot(ToothGrowth, aes(x=dose, y=len, color=dose)) +
geom_boxplot()
p
p+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))
p+scale_color_brewer(palette="Dark2")
改变箱颜色
p<-ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) +
geom_boxplot()
p
# Use custom color palettes
p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# use brewer color palettes
p+scale_fill_brewer(palette="Dark2")
# 改变横坐标展示顺序
p + scale_x_discrete(limits=c("2", "0.5", "1"))
多组展示
ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) +
geom_boxplot()
定制
bp <- ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) +
geom_boxplot()+
labs(title="Plot of length per dose",x="Dose (mg)", y = "Length")
bp + theme_classic()
bp + scale_fill_brewer(palette="Blues") + theme_classic()
bp + scale_fill_brewer(palette="Dark2") + theme_minimal()
violin plots
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
# trim
p <- ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_violin()
p
# no trim
p2<-ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_violin(trim=FALSE)
p2
显示范围
# 显示范围
p + scale_x_discrete(limits=c("0.5", "2"))
添加描述统计量
使用stat_summary()
# violin plot with mean points
p + stat_summary(fun.y=mean, geom="point", shape=23, size=2)
# 加箱线图
p + geom_boxplot(width=0.1)
修改颜色
和box plot 类似
p<-ggplot(ToothGrowth, aes(x=dose, y=len, color=dose)) +
geom_violin(trim=FALSE)
p
# Use custom color palettes
p+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Use brewer color palettes
p+scale_color_brewer(palette="Dark2")
定制
dp <- ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) +
geom_violin(trim=FALSE)+
geom_boxplot(width=0.1, fill="white")+
labs(title="Plot of length by dose",x="Dose (mg)", y = "Length")
dp
dp + scale_fill_brewer(palette="Blues") + theme_classic()
histogram 直方图
基础
#构造数据
set.seed(1234)
df <- data.frame(
sex=factor(rep(c("F", "M"), each=200)),
weight=round(c(rnorm(200, mean=55, sd=5), rnorm(200, mean=65, sd=5)))
)
# 基础
ggplot(df, aes(x=weight)) + geom_histogram()
# 加density
ggplot(df, aes(x=weight)) +
geom_histogram(aes(y=..density..), colour="black", fill="white")+
geom_density(alpha=.2, fill="#FF6666")
修改颜色并分组
# Change histogram plot line colors by groups
ggplot(df, aes(x=weight, color=sex)) +
geom_histogram(fill="white")
# Overlaid histograms
ggplot(df, aes(x=weight, color=sex)) +
geom_histogram(fill="white", alpha=0.7, position="identity")
ggplot(df, aes(x=weight, color=sex)) +
geom_histogram(fill="white", alpha=.7, position="dodge")
library(plyr)
mu <- ddply(df, "sex", summarise, grp.mean=mean(weight))
p<-ggplot(df, aes(x=weight, color=sex)) +
geom_histogram(fill="white", position="dodge")+
geom_vline(data=mu, aes(xintercept=grp.mean, color=sex),
linetype="dashed")+
theme(legend.position="top")
p
# Use custom color palettes
p+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Use brewer color palettes
p+scale_color_brewer(palette="Dark2")
填充
# Use semi-transparent fill
p<-ggplot(df, aes(x=weight, fill=sex, color=sex)) +
geom_histogram(position="identity", alpha=0.5)
p
p+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
定制
ggplot(df, aes(x=weight, color=sex, fill=sex)) +
geom_histogram(aes(y=..density..), position="identity", alpha=0.5)+
geom_density(alpha=0.6)+
geom_vline(data=mu, aes(xintercept=grp.mean, color=sex),
linetype="dashed")+
scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
labs(title="Weight histogram plot",x="Weight(kg)", y = "Density")+
theme_classic()
desnsity plot
p<-ggplot(df, aes(x=weight, fill=sex)) +
geom_density(alpha=0.4)
p
# Add mean lines
p+geom_vline(data=mu, aes(xintercept=grp.mean, color=sex),
linetype="dashed")
scatter plots
mtcars$cyl <- as.factor(mtcars$cyl)
# Change the point size
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point(aes(size=qsec))
# Add the regression line
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point()+
geom_smooth(method=lm)
# Remove the confidence interval
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point()+
geom_smooth(method=lm, se=FALSE)
# Loess method
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point()+
geom_smooth()
添加 Error bar
#+++++++++++++++++++++++++
# Function to calculate the mean and the standard deviation
# for each group
#+++++++++++++++++++++++++
# data : a data frame
# varname : the name of a column containing the variable
#to be summariezed
# groupnames : vector of column names to be used as
# grouping variables
data_summary <- function(data, varname, groupnames){
require(plyr)
summary_func <- function(x, col){
c(mean = mean(x[[col]], na.rm=TRUE),
sd = sd(x[[col]], na.rm=TRUE))
}
data_sum<-ddply(data, groupnames, .fun=summary_func,
varname)
data_sum <- rename(data_sum, c("mean" = varname))
return(data_sum)
}
df2 <- data_summary(ToothGrowth, varname="len",
groupnames=c("supp", "dose"))
# Convert dose to a factor variable
df2$dose=as.factor(df2$dose)
library(ggplot2)
# Default bar plot
p<- ggplot(df2, aes(x=dose, y=len, fill=supp)) +
geom_bar(stat="identity", color="black",
position=position_dodge()) +
geom_errorbar(aes(ymin=len-sd, ymax=len+sd), width=.2,
position=position_dodge(.9))
print(p)
# Finished bar plot
p+labs(title="Tooth length per dose", x="Dose (mg)", y = "Length")+
theme_classic() +
scale_fill_manual(values=c('#999999','#E69F00'))
# Default line plot
p<- ggplot(df2, aes(x=dose, y=len, group=supp, color=supp)) +
geom_line() +
geom_point()+
geom_errorbar(aes(ymin=len-sd, ymax=len+sd), width=.2,
position=position_dodge(0.05))
print(p)
# Finished line plot
p+labs(title="Tooth length per dose", x="Dose (mg)", y = "Length")+
theme_classic() +
scale_color_manual(values=c('#999999','#E69F00'))
资料来源
http://www.sthda.com/english/wiki/ggplot2-essentials
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