ggplot2版本
library(ggpubr)
library(scales)
library(Rmisc)
library(readxl)
library(RColorBrewer)
library(tidyverse)
area <- read_excel("./area.xlsx")
area_sum <- summarySE(area, measurevar="Value", groupvars=c("Group","Type"))
str(area_sum)
$ Group: Factor w/ 5 levels "WL+ND","WL+HFD",..: 1 1 1 2 2 2 4 4 4 5 ...
$ Type : num 1 2 3 1 2 3 1 2 3 1 ...
$ N : num 6 6 6 6 6 6 6 6 6 6 ...
$ Value: num 0.7534 0.2185 0.0281 0.5646 0.2823 ...
$ sd : num 0.0926 0.0888 0.0506 0.0438 0.0851 ...
$ se : num 0.0378 0.0362 0.0206 0.0179 0.0347 ...
$ ci : num 0.0972 0.0932 0.0531 0.046 0.0893 ...
ggplot(area_sum,aes(x=Type,y=Value,color=Group,fill=Group,shape=Group))+
geom_bar(stat ="identity",width = 0.8,fill="white",size=1.1,position = position_dodge(0.8),show.legend = F)+#柱状图
geom_errorbar(aes(ymin=Value, ymax=Value+sd), width=0.4,size=1.1,show.legend = F,position = position_dodge(0.8))+#误差棒
geom_jitter(size=1.5,alpha=0.8,position = position_jitterdodge(jitter.width = 0.5),data = area,show.legend = T)+#散点，加载原始数据及
annotate(geom = "text",
x=c(0.9,1.1,2.9),
y=c(0.68,0.65,0.3),
label=c("**","#","**"),
size=c(10,5,10))+#添加统计性，需另外计算
scale_color_manual(values = c("#bdbdbd","#636363","#31a354","#3182bd"))+
scale_fill_manual(values = c("#bdbdbd","#636363","#31a354","#3182bd"))+
scale_shape_manual(values = c(21,22,24,25))+
scale_y_continuous(expand = c(0,0),limits = c(0,1),labels = percent)+
scale_x_continuous(breaks=c(1,2,3),labels=c("<100","100~200",">200"))+
labs(y="Percent of islets",x="Diameter of islets (μm)")+
theme_classic()+
theme(axis.text=element_text(size=12,face = "bold",colour = "black"),
axis.title=element_text(size=12,face = "bold",colour = "black"),
axis.ticks.length=unit(.2, "cm"),
axis.line = element_line(colour = "black", size = 1.1),
axis.ticks = element_line(colour = "black", size = 1.1),
# legend.position = "none",
legend.title = element_blank(),
legend.text=element_text(size=12,face = "bold",colour = "black"),
strip.text = element_text(size=12,face = "bold",colour = "black"),
plot.title = element_text(hjust = 0.5,size = 14,face = "bold",colour = "black"))+
guides(fill = guide_legend(override.aes = list(size = 4)))
ggsave("islets-area_exclude.png",width = 10,height = 5)
ggpubr版本
ggbarplot(area, x="Type", y="Value",
add = c("mean_sd","jitter"),
size = 1.1,plot_type='l',
error.plot = "upper_errorbar",
color = "Group",fill="white",
add.params=list(color = "Group",shape = "Group",fill="Group",size=1.1),#无法单独为bar和dot赋予各自的属性，bar和dot的size合一出图太不美观了，而且bar的宽度也无法调整，难受
position = position_dodge(0.7))+
scale_color_manual(values = c("#bdbdbd","#636363","#31a354","#3182bd"))+
scale_fill_manual(values = c("#bdbdbd","#636363","#31a354","#3182bd"))+
scale_shape_manual(values = c(21,22,24,25))+
scale_y_continuous(expand = c(0,0),limits = c(0,1),labels = percent)+
scale_x_discrete(breaks=c(1,2,3),labels=c("<100","100~200",">200"))+#只能转换为离散型变量
labs(y="Percent of islets",x="Diameter of islets (μm)")+
theme_classic()+
theme(axis.text=element_text(size=12,face = "bold",colour = "black"),
axis.title=element_text(size=12,face = "bold",colour = "black"),
axis.ticks.length=unit(.2, "cm"),
axis.line = element_line(colour = "black", size = 1.1),
axis.ticks = element_line(colour = "black", size = 1.1),
legend.position = "none",
legend.title = element_blank(),
legend.text=element_text(size=12,face = "bold",colour = "black"),
strip.text = element_text(size=12,face = "bold",colour = "black"),
plot.title = element_text(hjust = 0.5,size = 14,face = "bold",colour = "black"))+
#stat_compare_means(aes(group=Group),label = "p.signif",label.y =0.9,method = "anova",hide.ns = T)
#此处显示的是全局p值，真正的p值还是需重新添加，添加方式参考https://github.com/const-ae/ggsignif或https://cran.r-project.org/web/packages/ggsignif/vignettes/intro.html
geom_signif(y_position=c(0.9,0.7, 0.3),
xmin=c(0.75,0.92,2.75),
xmax=c(0.92,1.09,2.92),
annotation=c("**","#","*"),
size = 1,
textsize = c(10,5,10,10,5,10,10,5,10),#3个数据，但只允许我提供1个或9个值，考虑到#号会比较大，建议缩小其对应的文本大小
tip_length=0.01)
一路看下来，还是ggplot2顺眼，想怎么调怎么调