ggplot2在线学习：STHDA ：Statistical tools for high-throughput data analysis.
ggplot2使用说明：https://ggplot2.tidyverse.org/reference/
- 火狐截图_2020-02-11T08-36-22.554Z.png
Dot Plot
根据说明文档，运行代码……
#convert the variable dose from a numeric to a factor variable
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
head(ToothGrowth)
#Basic dot plot
library(ggplot2)
p <- ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_dotplot(binaxis = 'y', stackdir = 'center')
p
#change the dot size and stack ratio
ggplot(ToothGrowth, aes(x=dose, y= len)) +
geom_dotplot(binaxis = 'y', stackdir = 'center',
stackratio = 1.5, dotsize = 1.2)
#Rotate the dot plot
p + coord_flip()
#chose the which items to display
p + scale_x_discrete(limit = c("0.5","2"))
#dot plot with mean points
p + stat_summary(fun.y = mean, geom = "point",shape = 8,
size = 3, color = "red")
#add basic box plot
ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_boxplot() +
geom_dotplot(binaxis = 'y', stackdir = "center")
#add notched box plot
ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_boxplot(notch = TRUE) +
geom_dotplot(binaxis = 'y', stackdir = "center")
#add violin plot
ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_violin(trim = FALSE) +
geom_dotplot(binaxis = 'y', stackdir = "center")
#add mean and standar deviation
p <- ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_dotplot(binaxis = 'y', stackdir = 'center')
p + stat_summary(fun.data = "mean_sdl",fun.args = list(mult = 1),
geom = "crossbar", width = 0.5)
p + stat_summary(fun.data = mean_sdl,fun.args = list(mult=1),
geom="pointrange", color ="red")
#function to produce summary statistic(mean and +/- sd)
data_summary <- function(x){
m <- mean(x)
ymin <- m - sd(x)
ymax <- m + sd(x)
return(c(y=m,ymin=ymin, ymax=ymax))
}
p + stat_summary(fun.data = data_summary, color = "blue")
#change the dot plot colors by group
#use the single fill color
ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_dotplot(binaxis='y', stackdir='center', fill="#FFAAD4")
# Change dot plot colors by groups
p<-ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) +
geom_dotplot(binaxis='y', stackdir='center')
p
# Use custom color palettes
p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Use brewer color palettes
p+scale_fill_brewer(palette="Dark2")
# Use grey scale
p + scale_fill_grey() + theme_classic()
#Change the legend position
p + theme(legend.position="top")
p + theme(legend.position="bottom")
p + theme(legend.position="none") # Remove legend
p + scale_x_discrete(limits=c("2", "0.5", "1"))
#dot plot with multiple groups
#change dot plot color by group
ggplot(ToothGrowth,aes(x=dose, y=len, fill=supp))+
geom_dotplot(binaxis = 'y', stackdir = "center")
#change the position : interval between dot plot of the same group
p <- ggplot(ToothGrowth,aes(x=dose, y=len, fill=supp))+
geom_dotplot(binaxis = 'y', stackdir = "center",
position = position_dodge(0.8))
p
#Change dot plot colors and add box plots :
# Change colors
p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Add box plots
ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) +
geom_boxplot(fill="white")+
geom_dotplot(binaxis='y', stackdir='center')
# Change the position
ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) +
geom_boxplot(position=position_dodge(0.8))+
geom_dotplot(binaxis='y', stackdir='center',
position=position_dodge(0.8))
#customized dot plots
# Basic dot plot
ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_boxplot()+
geom_dotplot(binaxis='y', stackdir='center')+
labs(title="Plot of length by dose",x="Dose (mg)", y = "Length")+
theme_classic()
# Change color by groups
dp <-ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) +
geom_dotplot(binaxis='y', stackdir='center')+
labs(title="Plot of length by dose",x="Dose (mg)", y = "Length")
dp + theme_classic()
#Change fill colors manually :
# Continuous colors.
dp + scale_fill_brewer(palette="Blues") + theme_classic()
# Discrete colors
dp + scale_fill_brewer(palette="Dark2") + theme_minimal()
# Gradient colors
dp + scale_fill_brewer(palette="RdBu") + theme_minimal()
