Today, I spent a lot of time sorting out the drawing functions of this package. I have to say that this package based on ggplot2 is really friendly and suitable for beginners. For those familiar with ggplot2, the existence of ggpubr may be redundant, but this does not prevent it from becoming an excellent R package.
Next, I will show about 10 functions and nearly 30 graphs of this package mainly based on variable types, covering almost most of the graphs I usually see. This tweet is also likely to be the most detailed ggpubr Chinese tutorial you’ve ever seen.
The official account is back to 20210330, obtaining today’s code and graphic example PDF.
install.packages("ggpubr")
library(ggpubr)
1. Single variable – continuous
1.1 density diagram
#Create data frame
set.seed(0330)
mydata = data.frame(
group = rep(c("A", "B","C","D"), each=200),
value = c(rnorm(200, mean = 2), rnorm(200, 6),rnorm(200,2,4),rnorm(200,6,4))
)
ggdensity(mydata, x = "value", y="..density..", # Or ".. count..", The default is ".. density.."
fill = "lightgray",
Add = "mean", # or "median",
Rug = true # adds a density line below the graph
)
ggsave("density1.pdf",width = 10,height = 10,units = "cm")
Group drawing
ggdensity(mydata, x = "value",
Color = "group", fill = "group", # group
Palette = "dark2", # or the color matching form of ggsci package such as "AAAs", or the encoding form of "#00afbb"
add = "mean",
rug = TRUE,
Alpha = 0.2, # adjust transparency
xlab=F,ylab = "Density",
facet. By = "group", # faceted
panel. Labels = list (group = C ("1", "2", "3", "4")), and # modify the name of each panel
,
ggtheme=theme_ BW () # can be a topic type in ggplot2
)
ggsave("density2.pdf",width = 13,height = 12,units = "cm")
1.2 density map superimposed normal distribution
set.seed(0330)
mydata = data.frame(
group = rep(c("A", "B"), each=200),
value = c(rnorm(200, 2), rnorm(200, 6, 4))
)
ggdensity(mydata, x = "value", fill = "red") +
stat_overlay_normal_density(color = "red", linetype = "dashed")+
scale_x_continuous(limits = c(-5,20))
ggsave("density3.pdf",width = 10,height = 10,units = "cm")
Group drawing
ggdensity(mydata, x = "value", fill = "group") +
stat_overlay_normal_density(aes(color=group), linetype = "dashed")+
scale_x_continuous(limits = c(-5,20))
ggsave("density4.pdf",width = 10,height = 10,units = "cm")
Grouping + faceting
ggdensity(mydata, x = "value", fill = "group", facet.by = "group") +
stat_overlay_normal_density(aes(color=group), linetype = "dashed")+
scale_x_continuous(limits = c(-5,20))
ggsave("density5.pdf",width = 16,height = 10,units = "cm")
1.3 histogram
gghistogram(mydata, x = "value", fill = "lightgray",
add = "mean", rug = TRUE)
ggsave("hist1.pdf",width = 10,height = 10,units = "cm")
Group drawing
gghistogram(mydata, x = "value", fill = "group",
add = "mean", rug = TRUE,
palette = c("#00AFBB", "#E7B800"))
ggsave("hist2.pdf",width = 10,height = 10,units = "cm")
Add nuclear density map
gghistogram(mydata, x = "value", fill = "group",
rug = TRUE,
palette = c("#00AFBB", "#E7B800"),
add_density = TRUE)
ggsave("hist3.pdf",width = 10,height = 10,units = "cm")
2. Bivariate – x discrete, y continuous
2.1 box diagram
library(patchwork)
set.seed(0330)
mydata = data.frame(
group = rep(c("A", "B"), each=100),
group2 = rep(c("g1","g2","g1","g2"),each=50),
value = c(rnorm(100, 2), rnorm(100, 6, 4))
)
#The following plus sign indicates the splicing figure
ggboxplot(mydata, x = "group", y = "value", width = 0.8)+
ggboxplot(mydata, x = "group", y = "value", width = 0.8, orientation = "horizontal")+
ggboxplot(mydata, x = "group", y = "value", width = 0.8, notch = TRUE,order = c("B","A"))+
ggboxplot(mydata, x = "group", y = "value", width = 0.8, select = c("A"))
ggsave("box1.pdf",width = 10,height = 10,units = "cm")Orientation: adjust the direction of the drawing; Notch add gap; Order adjustment order; Select select a specific level to draw
ggboxplot(mydata, x = "group", y = "value", width = 0.8, add = "jitter",add.params=list(color = "lightblue",size=1, shape = 17))+
ggboxplot(mydata, x = "group", y = "value", width = 0.8, add = "dotplot",add.params=list(color = "lightblue",size=0.5))
ggsave("box2.pdf",width = 16,height = 10,units = "cm")
Add additional graphics above
add. Params adjusts the parameters of additional graphics. Shape represents the shape of points, which can be seen in the following figure
Internal grouping
ggboxplot(mydata, x = "group", y = "value", width = 0.6, color = "black",fill="group2",palette = c("#00AFBB", "#E7B800"),
Xlab = f, # does not display the label of X axis
bxp. errorbar=T,bxp. errorbar. Width = 0.4, # add errorbar
Size = 1, # box type drawing edge line thickness
outlier. Shape = Na, # do not display outlier
Legend = "right") # legend on the right
ggsave("box3.pdf",width = 10,height = 10,units = "cm")
2.1.1 add pairing connection to box diagram
Two data frames are acceptable
mydata2=mydata
mydata2$group2=NULL
head(mydata2)
# group value
# 1 A 3.551687
# 2 A 3.664068
# 3 A 2.194454
# 4 A 2.569605
# 5 A 2.579997
# 6 A 1.837967
ggpaired(mydata2, x = "group", y = "value",
color = "group", line.color = "gray", line.size = 0.4,
palette = "npg")
mydata2$id=rep(1:100,2)
mydata2=mydata2%>%reshape2::dcast(id~group)
head(mydata2)
# id A B
# 1 1 3.551687 4.720074
# 2 2 3.664068 7.821049
# 3 3 2.194454 8.956841
# 4 4 2.569605 -4.450063
# 5 5 2.579997 7.568216
# 6 6 1.837967 5.133688
ggpaired(mydata2, cond1 = "A", cond2 = "B",
color = "condition", line.color = "gray", line.size = 0.4,
palette = "npg")
ggsave("box4.pdf",width = 10,height = 10,units = "cm")
The two data frames as like as two peas are identical.
2.1.2 add p value
General usage
ggboxplot(mydata, x = "group", y = "value", width = 0.8,
add = "dotplot",add.params=list(color = "lightblue",size=0.5))+
stat_compare_means(method = "t.test")
ggsave("box5.pdf",width = 10,height = 10,units = "cm")
Paired data
ggpaired(mydata2, cond1 = "A", cond2 = "B",
color = "condition", line.color = "gray", line.size = 0.4,
palette = "npg")+
stat_compare_means(paired = TRUE)
ggsave("box6.pdf",width = 10,height = 10,units = "cm")
When there are more than two groups, define the pairing to be tested
my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
ggboxplot(ToothGrowth, x = "dose", y = "len",
color = "dose", palette = "npg")+
#P value of pairwise comparison
stat_compare_means(comparisons = my_comparisons, label.y = c(29, 35, 40))+
#Overall p value
stat_compare_means(label.y = 45)
ggsave("box7.pdf",width = 10,height = 10,units = "cm")
Fix one group and compare with other groups
ggboxplot(ToothGrowth, x = "dose", y = "len",
color = "dose", palette = "npg")+
#Overall p value
stat_compare_means(method = "anova", label.y = 40)+
#The significance is represented by dots in label
stat_compare_means(aes(label = ..p.signif..),
method = "t.test", ref.group = "0.5")
ggsave("box8.pdf",width = 10,height = 10,units = "cm")
Compare after grouping / faceting
ggboxplot(ToothGrowth, x = "supp", y = "len",
color = "supp", palette = "npg",
add = "jitter",
facet.by = "dose")+
#Remove the inspection method from the label
stat_compare_means(aes(label = paste0("p = ", ..p.format..)))
ggsave("box9.pdf",width = 10,height = 10,units = "cm")
2.2 violin drawing
On the whole, the parameter options are similar to the box diagram
ggviolin(mydata, x = "group", y = "value", fill = "group",
palette = c("#00AFBB", "#E7B800"),
add = "boxplot", add.params = list(fill = "white"))+
Ggviolin (mydata, x = "group", y = "value", color = "group2", # internal grouping)
palette = c("#00AFBB", "#E7B800"),
add = "boxplot")
ggsave("violin1.pdf",width = 16,height = 10,units = "cm")
2.3 column diagram
2.3.1 data have been counted
df1 <- data.frame(group=c("A", "B", "C"),
len=c(6, 10, 14))
ggbarplot(df1, "group", "len",
fill = "group", color = "group",
palette = c("#00AFBB", "#E7B800", "#FC4E07"),
label = TRUE, lab.pos = "in", lab.col = "white")
ggsave("bar1.pdf",width = 10,height = 10,units = "cm")
2.3.2 poor statistics
(you need a function to help you calculate, such as summation within a group, which is generally reflected in the ordinate, which is calculated by the function)
df2 <- data.frame(group=rep(c("A", "B", "C"),2),
group2=rep(c("1", "2"), each=3),
len=c(6, 15, 3, 4, 10, 5))
# group group2 len
# 1 A 1 6
# 2 B 1 15
# 3 C 1 3
# 4 A 2 4
# 5 B 2 10
# 6 C 2 5
ggbarplot(df2, "group", "len",
fill = "group2", color = "group2", palette = "Paired",
label = TRUE, lab.col = "white", lab.pos = "in")+
ggbarplot(df2, "group", "len",
fill = "group2", color = "group2", palette = "Paired",
label = TRUE,
position = position_ Dodge (0.9)) # range 0-1, indicating the degree of staggering between columns
ggsave("bar2.pdf",width = 16,height = 10,units = "cm")
2.3.3 add error bar
df3 <- mydata
#Then accumulate
ggbarplot(df3, x = "group", y = "value")+
#Then find the mean
ggbarplot(df3, x = "group", y = "value",
add = "mean")+
#Add error bar, error Plot select the display form, which is displayed up and down by default
ggbarplot(df3, x = "group", y = "value",
add = "mean_se",
error.plot = "upper_errorbar")+
#Internal grouping
ggbarplot(df3, x = "group", y = "value", color = "group2",
add = "mean_se", palette = c("#00AFBB", "#E7B800"),
position = position_dodge())
ggsave("bar3.pdf",width = 16,height = 16,units = "cm")
2.4 wiring diagram
#The data is well calculated and can be used directly
ggline(df1, x = "group", y = "len")+
#Internal grouping, dotted lines have different shapes and colors
ggline(df2, x = "group", y = "len",
Linetype = "group2", shape = "group2", # point shape
color = "group2", palette = c("#00AFBB", "#E7B800"))+
#Add points and error bars
ggline(df3, x = "group", y = "value",
add = c("mean_se","dotplot"),add.params = list(size=0.5),
color = "steelblue")+
#For internal grouping, the color of lines is different
ggline(df3, x = "group", y = "value", color = "group2",
add = "mean_se", palette = c("#00AFBB", "#E7B800"))
ggsave("line1.pdf",width = 16,height = 16,units = "cm")
2.5 pie chart
df1$ratio=paste(df1$group,"(",round(df1$len / sum(df1$len),3) * 100,"%)",sep = "")
ggpie(df1, "len", label = "ratio",
fill = "group", color = "white",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))+
ggpie(df1, "len", label = "ratio",
lab.pos = "in", lab.font = "white",
fill = "group", color = "white",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
ggsave("pie1.pdf",width = 16,height = 10,units = "cm")
Add text annotation to label;
Color is the edge of the fan. Lab.pos adjusts the position of the text and lab.font adjusts the font color of the text
2.6 ring diagram
ggdonutchart(df1, "len", label = "ratio",
lab.pos = "in", lab.font = "white",
fill = "group", color = "white",
palette = c("#00AFBB", "#E7B800", "#FC4E07"))
ggsave("donut1.pdf",width = 10,height = 10,units = "cm")
2.7 Cleveland point map
ggdotchart(df2, x = "group", y = "len",
color = "group2", size = 3,
add = "segment",
add.params = list(color = "lightgray", size = 1.5),
position = position_dodge(0.5),
palette = "jco",
ggtheme = theme_pubclean())
ggsave("Clevelands_Dot1.pdf",width = 10,height = 10,units = "cm")
3. Bivariate – x, y are continuous
3.1 adding regression line and correlation coefficient to scatter diagram
df4=mtcars
df4$cyl=as.factor(df4$cyl)
ggscatter(df4, x = "wt", y = "mpg",
Color = "black", size = 3, # point color, size
Add = "reg. Line", # add regression line
add. Params = list (color = "blue", fill = "lightgray"), # regression line adjustment
Conf.int = true, # confidence interval of regression line
Cor.coef = true, # add correlation coefficient
cor.coeff. Args = list (method = "Pearson", label. X = 3, label. SEP = "\ n") # correlation coefficient adjustment
)3.2 group calculation of correlation coefficient
ggscatter(df4, x = "wt", y = "mpg",
color = "cyl", palette = "jco",
add = "reg.line", conf.int = TRUE)+
stat_cor(aes(color = cyl), label.x = 3)
3.3 local regression
ggscatter(df4, x = "wt", y = "mpg",
add = "loess", conf.int = TRUE)
3.4 add grouping ellipses, mean points, and radiation lines
ggscatter(df4, x = "wt", y = "mpg",
color = "cyl", shape = "cyl",
palette = c("#00AFBB", "#E7B800", "#FC4E07"),
ellipse = TRUE, mean.point = TRUE,
star.plot = TRUE)
3.5 adding text notes
df4$name <- rownames(df4)
ggscatter(df4, x = "wt", y = "mpg",
color = "cyl", palette = c("#00AFBB", "#E7B800", "#FC4E07"),
label = "name", repel = TRUE)+plot_layout(widths = c(1,2))
3.6 scatter chart edge addition density chart / box chart
ggscatterhist(
iris, x = "Sepal.Length", y = "Sepal.Width",
color = "Species", size = 3, alpha = 0.6,
palette = c("#00AFBB", "#E7B800", "#FC4E07"),
margin.params = list(fill = "Species", color = "black", size = 0.2)
)
ggscatterhist(
iris, x = "Sepal.Length", y = "Sepal.Width",
color = "Species", size = 3, alpha = 0.6,
palette = c("#00AFBB", "#E7B800", "#FC4E07"),
margin.plot = "boxplot",
ggtheme = theme_bw()
)
Thank you for reading here. If you have any questions, please leave a message backstage.
Due to the limited level, there are mistakes, welcome criticism and correction!