---

When creating graphs using data, especially those involving error bars, it is necessary to calculate the standard error by summarizing the data. There are various methods to summarize the data.

---

□ Utilizing R Studio for Data Grouping and Mean/Standard Error Calculation (feat ddply)

---

Today I will introduce a method of creating graphs all at once using stat_summary() without the need for such data summarization.

Below is an example dataset:

Genotype= c(rep(c("CV1","CV2"),each=20))
position= rep(paste(1:20),times=2)
Block= c(rep(c("I","II","III"),each=40))
number= c(2,3,3,3,3,3,4,4,4,4,4,4,4,3,3,4,3,2,2,2,
          3,3,3,3,4,3,3,3,4,5,4,3,4,5,3,3,3,2,3,1,
          1,3,4,3,2,3,3,3,4,4,5,4,3,3,3,2,3,2,2,3,
          2,3,4,3,2,3,4,4,4,4,4,4,4,3,3,3,3,2,1,1,
          2,3,3,3,2,2,5,3,4,5,4,5,4,3,2,5,4,2,2,2,
          1,3,3,3,4,3,3,4,4,4,4,3,4,3,2,1,3,2,4,2)
dataA= data.frame(Genotype,position,Block,number)
dataA

---

---

Now I want to display the data as points by placing the x-axis at “position” and the y-axis at “number.”

library(ggplot2)
ggplot(data=dataA) +
  stat_summary(aes(x=as.numeric(position), y=as.numeric(number), fill=Genotype,
                   shape=Genotype), geom="point", fun = mean, col="Black", size=5)+ 
  scale_fill_manual(values= c("black","red")) +
  scale_shape_manual(values= c(21,22)) +
  scale_x_continuous(breaks= seq(0,21,2),limits= c(0,21)) +
  scale_y_continuous(breaks= seq(0,5,1),limits= c(0,5)) +
  labs(fill= "Genotype", x="Position", y='Grain number') +
  theme_classic(base_size=20, base_family="serif")+
  theme(legend.position=c(0.90,0.12),,
        legend.title=element_blank(),
        legend.key.size=unit(0.5,'cm'),
        legend.key=element_rect(color=alpha("white",.05), 
                                fill=alpha("white",.05)),
        legend.text=element_text(size=11),
        legend.background= element_rect(fill=alpha("white",.05)),
        panel.grid.major=element_line(colour="grey90", linewidth=0.5),
        axis.line=element_line(linewidth=0.5, colour="black")) +
windows(width=5.5, height=5) 

I’ve created the graph like above.

---

---

Now I want to add error bars. So, I’ll insert the following code:

library(ggplot2)
ggplot(data=dataA) +
  stat_summary(aes(x=as.numeric(position), y=as.numeric(number), fill=Genotype,
                   shape=Genotype), geom="point", fun= mean, col="Black", size=5)+ 
  stat_summary(aes(x=as.numeric(position), y=as.numeric(number), group=Genotype),
               geom="errorbar", col="Black", width=.8)+
  scale_fill_manual(values= c("black","red")) +
  scale_shape_manual(values= c(21,22)) +
  scale_x_continuous(breaks= seq(0,21,2),limits= c(0,21)) +
  scale_y_continuous(breaks= seq(0,5,1),limits= c(0,5)) +
  labs(fill= "Genotype", x="Position", y='Grain number') +
  theme_classic(base_size=20, base_family="serif")+
  theme(legend.position=c(0.90,0.12),,
        legend.title=element_blank(),
        legend.key.size=unit(0.5,'cm'),
        legend.key=element_rect(color=alpha("white",.05), 
                                fill=alpha("white",.05)),
        legend.text=element_text(size=11),
        legend.background= element_rect(fill=alpha("white",.05)),
        panel.grid.major=element_line(colour="grey90", linewidth=0.5),
        axis.line=element_line(linewidth=0.5, colour="black")) +
windows(width=5.5, height=5)           

---

---

I want to connect the points with lines. So, I’ll add the following code:

library(ggplot2)
ggplot(data=dataA) +
  stat_summary(aes(x=as.numeric(position), y=as.numeric(number), fill=Genotype,
                   shape=Genotype), geom="point", fun = mean, col="Black", size=5)+ 
  stat_summary(aes(x=as.numeric(position), y=as.numeric(number), group=Genotype),
               geom="errorbar", col="Black", width=.8)+
  stat_summary(aes(x=as.numeric(position), y=as.numeric(number), group=Genotype),
               geom="line", fun= mean, lty="dashed")+ 
  scale_fill_manual(values= c("black","red")) +
  scale_shape_manual(values= c(21,22)) +
  scale_x_continuous(breaks= seq(0,21,2),limits = c(0,21)) +
  scale_y_continuous(breaks= seq(0,5,1),limits = c(0,5)) +
  labs(fill= "Genotype", x="Position", y='Grain number') +
  theme_classic(base_size=20, base_family="serif")+
  theme(legend.position=c(0.90,0.12),,
        legend.title=element_blank(),
        legend.key.size=unit(0.5,'cm'),
        legend.key=element_rect(color=alpha("white",.05), 
                                fill=alpha("white",.05)),
        legend.text=element_text(size=11),
        legend.background= element_rect(fill=alpha("white",.05)),
        panel.grid.major=element_line(colour="grey90", linewidth=0.5),
        axis.line=element_line(linewidth=0.5, colour="black")) +
windows(width=5.5, height=5)

---

---

Now I want to rotate the graph. So, I’ll add the following code using coord_flip()

library(ggplot2)
ggplot(data=dataA) +
  stat_summary(aes(x=as.numeric(position), y=as.numeric(number), fill=Genotype,
                   shape=Genotype), geom="point", fun = mean, col="Black", size=5)+ 
  stat_summary(aes(x=as.numeric(position), y=as.numeric(number), group=Genotype),
               geom="errorbar", col="Black", width=.8)+
  stat_summary(aes(x=as.numeric(position), y=as.numeric(number), group=Genotype),
               geom="line", fun= mean, lty="dashed")+ 
  scale_fill_manual(values= c("black","red")) +
  scale_shape_manual(values= c(21,22)) +
  scale_x_continuous(breaks= seq(0,21,2),limits = c(0,21)) +
  scale_y_continuous(breaks= seq(0,5,1),limits = c(0,5)) +
  coord_flip() +
  labs(fill= "Genotype", x="Position", y='Grain number') +
  theme_classic(base_size=20, base_family="serif")+
  theme(legend.position=c(0.90,0.12),,
        legend.title=element_blank(),
        legend.key.size=unit(0.5,'cm'),
        legend.key=element_rect(color=alpha("white",.05), 
                                fill=alpha("white",.05)),
        legend.text=element_text(size=11),
        legend.background= element_rect(fill=alpha("white",.05)),
        panel.grid.major=element_line(colour="grey90", linewidth=0.5),
        axis.line=element_line(linewidth=0.5, colour="black")) +
windows(width=5.5, height=5) 

---

---