ggplot2 geom_jitter

library(ggplot2)
All <- read.csv("~/00-NGS/RNAseq/bov/niceM/Sham_Corrected/TopHat_UMD3.1_NCBI/log10_log2_mean.csv")
colnames(All) = c("chr","MI","MN","FI","FN",
                  "log10_MN_MI","log10_FI_MI","log10_FN_MI",
                  "log2_MN_MI","log2_FI_MI","log2_FN_MI")
head(All)

# set chr in natural order
All$chr <- factor(All$chr, 
                  levels=c("1","2","3","4","5","6","7","8","9","10",
                  "11","12","13","14","15","16","17","18","19","20",
                  "21","22","23","24","25","26","27","28","29","X"))

# draw jitter plots
ggplot(All,aes(x=chr,y=log10_MN.MI)) 
+ geom_jitter(alpha=0.5, position=position_jitter(width=0.35)), aes(color=chr), size=2) 
#+ geom_boxplot()  # if you want to overlap with boxplots


# overlyed jitter plot
ggplot(All,aes(x=chr,y=log10_FI.MI))+guides(colour=FALSE)+ylim(c(-1.5,1.5))
+geom_jitter(alpha=1,size=2,position=position_jitter(width=0.4),aes(color="blue"))
+geom_jitter(data=All,aes(x=chr,y=log10_FN.MI,color="red"),alpha=0.5,size=2,position=position_jitter(width=0.4))
+geom_jitter(data=All,aes(x=chr,y=log10_MN.MI),alpha=0.5,size=2,position=position_jitter(width=0.4))