Rplot

#!/usr/bin/Rscript
library(ggplot2)

cf = read.table(file = 'result_sort.txt', header = TRUE, sep=' ')
cf$col = factor(cf$col, levels = c(
"siginificant detected Proteins according to filter criteria",
"Proteins fit to criteria 1-3",
"Proteins not fit to filter criteria"
))

p = ggplot(cf, aes(x = control , y = Experiment ,color=col))
p + geom_point(size=5,shape=18,alpha=0.7) +
scale_colour_manual(values = c("red",'green','black')) +
theme(panel.background = element_blank(),panel.border=element_rect(fill='transparent', color='black')) +
theme(legend.title=element_blank(),legend.position='none') +
#coord_fixed(ratio = 1) +
geom_abline(slope = 1,intercept = 0) +
scale_x_continuous(trans='log2',breaks=c(1,2,4,8,16,32,64,128,256),limit=c(1,281)) +
scale_y_continuous(trans='log2',breaks=c(1,2,4,8,16,32,64,128,256),limit=c(1,281)) +
labs(x="Peptide counts (controls)",y="Peptide counts (expreiments)")

#geom_hline(yintercept=c(1,2,4,8,16,32,64,128,256), size = 0.3)