## 2Dplus
## 2d plot plus coloring with 3rd variable
## 2d+
library(ggplot2)
# p + geom_point(aes(x = Male.Het.H3K9me3, y = Male.KO.H3K9me3, color = Male.Het.H3K27me3),
# alpha = 1/2) + theme_classic()
#
#
#
# load("~/DoScience/DoScience/Projects/PGC project/PGCs/Data/3-SeqData/BSseq/Data/2014-03-06/K9K27.gated.sp.rda")
#
# names(K9K27.gated.sp)
# p = ggplot(K9K27.gated.sp)
# p + geom_point(aes(x = Male.Het.H3K9me3, y = Male.KO.H3K9me3, color = Male.Het.H3K27me3),
# alpha = 1/2) + theme_classic()
#
#
# xyplot(Male.KO.H3K9me3~Male.Het.H3K9me3,data=K9K27.gated.sp)
#
#
# xyplot(Male.KO.H3K9me3~Male.Het.H3K9me3,data=K9K27.gated.sp)
# p+geom_point(aes(x=Male.Het.H3K27me3,y=Male.KO.H3K27me3,color=Male.Het.H3K9me3))+
# theme_classic()+
# theme_classic()+scale_color_gradient(low = "black", high = "yellow")+
# theme(legend.background=element_blank())
DDplus.plot=function(action,window){
library(ggplot2)
print("2D+ plot")
select.channels(channelZ=T)
x=appspace[channelX]
y=appspace[channelY]
z=appspace[channelZ]
df=as.data.frame(exprs(appspace[active.SeqFrame]))
p=ggplot(df)
p=p+
theme_classic()+
scale_color_gradient(low = "black", high = "yellow")+
theme(legend.background=element_blank())
f=sprintf("p+geom_point(aes(x=`%s`,y=`%s`,color=`%s`))",x,y,z)
# parse(text = f)
dev.new(width=6,height=4)
print(eval(parse(text=f)))
}
# quote(x)
# x=deparse(substitute(x))
# y=deparse(substitute(y))
# z=deparse(substitute(z))
#
# x=as.symbol(x)
# y=as.symbol(y)
# z=as.symbol(z)
#
# x=print(x,quote=F)
# x=deparse(substitute(appspace[channelX]))
# y=
# p+geom_point(aes(x="Male.Het.DNAme",y="Male.KO.DNAme",color="Male.KO.DNAme"))
#
#
#
#
#
# p+geom_point(aes(x=Male.Het.H3K27me3,y=Male.KO.H3K27me3,color=Male.Het.H3K9me3))+
# theme_classic()+
# theme_classic()+scale_color_gradient(low = "black", high = "yellow")+
# theme(legend.background=element_blank())+
# theme(legend.position=c(0,1), legend.justification=c(0,0.9))
## add minor ticks
addMinorTicks=function(start,end,by){
minor.ticks=seq(start,end,by=by)
major.ticks=seq(start,end,by=by*2)
blank.ticks=setdiff(minor.ticks,major.ticks)
blank.index=c()
for (i in 1:length(blank.ticks)){
blank=which(minor.ticks==blank.ticks[i])
blank.index=c(blank.index,blank)
}
minor.ticks.label=replace(minor.ticks,blank.index," ")
return(minor.ticks.label)
}
# last_plot()+scale_y_continuous(breaks=c(seq(0,100,by=5)),labels=addMinorTicks(0,100,10))
# try use lattice to do the same, but only works on catogorical ones
# it will be multipannel though, kind of like ggplot2
##FIXME:
## plot with different pannel for catogorical varaibles
# p <- ggplot(mtcars, aes(disp, mpg))
# p + geom_point() + facet_grid(.~gear)
#
# f=sprintf("p+geom_point(aes(x=`%s`,y=`%s`))+facet_grid(.~`%s`)",x,y,z)
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