scatterplot

#CD45+
View(treated)
ggplot(treated, aes(x=Mice, y=CD45 )) +
  geom_point(size=2, shape=23)

#CD3+
ggplot(data=treated, aes(x=Mice , y=CD3 ))+
  geom_point() + xlab('Mice')

#CD4+
ggplot(data=treated, aes(x=Mice , y=CD4 ))+
  geom_point() + xlab('Mice')

#CD4+/FOXP3+
ggplot(data=treated, aes(x=Mice , y= CD4FOXP3 ))+
  geom_point() + xlab('Mice')

#CD8
ggplot(data=treated, aes(x=Mice , y=CD8 ))+
  geom_point() + xlab('Mice')

#CD45+
View(untreated)
ggplot(untreated, aes(x=Mice, y=CD45 )) +
  geom_point(size=2, shape=23)

#CD3+
ggplot(data=untreated, aes(x=Mice , y=CD3 ))+
  geom_point() + xlab('Mice')

#CD4+
ggplot(data=untreated, aes(x=Mice , y=CD4 ))+
  geom_point() + xlab('Mice')

#CD4+/FOXP3+
ggplot(data=untreated, aes(x=Mice , y= CD4FOXP3 ))+
  geom_point() + xlab('Mice')

#CD8
ggplot(data=untreated, aes(x=Mice , y=CD8 ))+
  geom_point() + xlab('Mice')

View(untreated_and_treated)
#CD45+
ggplot(data=untreated_and_treated, aes(x=Mice , y=CD45 , color= Treatment))+
  geom_point() + xlab('Mice')

#CD3+
ggplot(data=untreated_and_treated, aes(x=Mice , y=CD3 , color= Treatment))+
  geom_point() + xlab('Mice')

#CD4+
ggplot(data=untreated_and_treated, aes(x=Mice , y=CD4 , color= Treatment))+
  geom_point() + xlab('Mice')

#CD4+/FOXP3+
ggplot(data=untreated_and_treated, aes(x=Mice , y=CD4FOXP3 , color= Treatment))+
  geom_point() + xlab('Mice')

#CD8
ggplot(data=untreated_and_treated, aes(x=Mice , y=CD8 , color= Treatment))+
  geom_point() + xlab('Mice')

#box and whisker plot without 0.25 and 0.75 lines
View(untreated_and_treated)
ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD45", 
            desc_stat = "mean_sd")

ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD3", 
            desc_stat = "mean_sd")

ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD4", 
            desc_stat = "mean_sd")

ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD4FOXP3", 
            desc_stat = "mean_sd")

ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD8", 
            desc_stat = "mean_sd")

#box and whisker plot with 0.25 and 0.75 lines
ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD45", 
            desc_stat = "mean_sd",
            error.plot = "errorbar",            
            add = "mean")

`fun.y` is deprecated. Use `fun` instead.`fun.ymin` is deprecated. Use `fun.min` instead.`fun.ymax` is deprecated. Use `fun.max` instead.

ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD3", 
            desc_stat = "mean_sd",
            error.plot = "errorbar",            
            add = "mean")

`fun.y` is deprecated. Use `fun` instead.`fun.ymin` is deprecated. Use `fun.min` instead.`fun.ymax` is deprecated. Use `fun.max` instead.

ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD4", 
            desc_stat = "mean_sd",
            error.plot = "errorbar",            
            add = "mean")

`fun.y` is deprecated. Use `fun` instead.`fun.ymin` is deprecated. Use `fun.min` instead.`fun.ymax` is deprecated. Use `fun.max` instead.

ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD4FOXP3", 
            desc_stat = "mean_sd",
            error.plot = "errorbar",            
            add = "mean")

`fun.y` is deprecated. Use `fun` instead.`fun.ymin` is deprecated. Use `fun.min` instead.`fun.ymax` is deprecated. Use `fun.max` instead.

ggerrorplot(untreated_and_treated, x = "Treatment", y = "CD8", 
            desc_stat = "mean_sd",
            error.plot = "errorbar",            
            add = "mean")

`fun.y` is deprecated. Use `fun` instead.`fun.ymin` is deprecated. Use `fun.min` instead.`fun.ymax` is deprecated. Use `fun.max` instead.

#box and whisker plot  colored box 
ggplot(untreated_and_treated, aes(x=as.factor(Treatment), y=CD45)) + 
  geom_boxplot(fill="slateblue", alpha=0.2) + 
  xlab("Treatment")

ggplot(untreated_and_treated, aes(x=as.factor(Treatment), y=CD4)) + 
  geom_boxplot(fill="slateblue", alpha=0.2) + 
  xlab("Treatment")

ggplot(untreated_and_treated, aes(x=as.factor(Treatment), y=CD3)) + 
  geom_boxplot(fill="slateblue", alpha=0.2) + 
  xlab("Treatment")

ggplot(untreated_and_treated, aes(x=as.factor(Treatment), y=CD4FOXP3)) + 
  geom_boxplot(fill="slateblue", alpha=0.2) + 
  xlab("Treatment")

ggplot(untreated_and_treated, aes(x=as.factor(Treatment), y=CD8)) + 
  geom_boxplot(fill="slateblue", alpha=0.2) + 
  xlab("Treatment")

#box plot with individual points 

There were 35 warnings (use warnings() to see them)

a <- ggplot(untreated_and_treated, aes(Treatment, CD45))
a + geom_boxplot(outlier.shape = NA) + geom_jitter(width = 0.2)

b <- ggplot(untreated_and_treated, aes(Treatment, CD4))
b + geom_boxplot(outlier.shape = NA) + geom_jitter(width = 0.2)

c <- ggplot(untreated_and_treated, aes(Treatment, CD3))
c + geom_boxplot(outlier.shape = NA) + geom_jitter(width = 0.2)

d <- ggplot(untreated_and_treated, aes(Treatment, CD4FOXP3))
d + geom_boxplot(outlier.shape = NA) + geom_jitter(width = 0.2)

e <- ggplot(untreated_and_treated, aes(Treatment, CD8))
e + geom_boxplot(outlier.shape = NA) + geom_jitter(width = 0.2)