more boxplots

library(ggplot2)
library(ggpmisc)
library(ggpubr)
library(ggrepel)
library(reshape2)

setwd("~/BIO2/DAM_ID/DamID_2018/SE/mm9")
setwd("~/BIO2/DAM_ID/RNAseq_shDnmt1/mm9")

te = "LINE.5kb"
te = "ERVL.1kb"
dta <- read.delim(paste("cnt.",te,".elements.aggregate.tsv",sep=""), header = F)
#dta <- read.delim(paste("cnt.",te,".top10.copyNumber.elements.tsv",sep=""), header = F)
#dta <- read.delim(paste("cnt.",te,".cnt2.top10",sep=""), header = F)
#dta <- read.delim(paste("cnt.",te,".cnt.agg2",sep=""), header = F)
#colnames(dta) <- c("name","Dnmt1","Dam")
colnames(dta) <- c("name","siDnmt1","siScrb")
head(dta)

dta2 <- dta[rowMeans(dta[,2:3]) > 0,]
mdta <- melt(dta2)
head(mdta)
mdta

means <- aggregate(value ~  variable, mdta, mean)
log2(means[,2])

ggplot(mdta, aes(x=factor(variable), y=log2(value+1))) + theme_bw() +
  geom_boxplot(width =.3, outlier.shape = NA) +
  stat_summary(fun.y=mean, geom="point", shape=18, size=5, color="red") +


dev.off()
ggplot(mdta, aes(x=factor(variable), y=log2(value))) + theme_bw() +
  geom_jitter(aes(fill=variable),width=.3) +
  geom_line(group = mdta$name, color="grey50") +
  geom_violin(aes(fill=variable, alpha=.3)) +
  geom_boxplot(width =.3, outlier.shape = NA) +
  stat_summary(fun.y=mean, geom="point", shape=18, size=5, color="red") +
  stat_compare_means(size = 5, label.x.npc = .2,label.y = 21) +
  stat_summary(fun.y=mean, colour="black", geom="text", show.legend = FALSE, size=4.5, vjust=-1, aes( label=round(..y.., digits=2))) +
  scale_fill_manual(values=c("orange", "darkgreen")) +
  theme(axis.title.y=element_blank(),axis.title.x=element_blank(), 
        axis.text.x=element_blank(), axis.ticks.x=element_blank(),legend.position="none")

  #scale_fill_manual(values=c("salmon", "steelblue"))+
  #geom_point(aes(fill=variable),color="white") +
  #stat_compare_means(aes(label=..p.adj..)) + #, label.y = 15) +
  #scale_fill_manual(values=c("orange", "darkgreen")) +
  #geom_text(aes(label=name),hjust=0, vjust=1, size = 3)


dev.off()
ggplot(mdta, aes(x=factor(variable), y=log2(1+value))) + theme_bw() +
  geom_jitter(aes(fill=variable), alpha=.3, size = 1, color ="grey50") +
  geom_violin(aes(fill=variable, group=variable), alpha=.4) +
  #facet_grid(~name, scales = "free", space = "free_y") +
  facet_wrap(~name, scales="free", ncol = 5) + #theme(aspect.ratio = 1) +
  theme(strip.text.x = element_text(size = 12)) + 
  theme(axis.title.y=element_blank(),axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank(),legend.position="none") +
  stat_summary(fun.y=mean, geom="point", shape=18, size=3, color="red") +
  stat_summary(fun.y=mean, geom="line", color="red", size=1, aes(group=1))  + 
  stat_compare_means(label="p.signif", hide.ns=T,  size=10, label.x.npc= .1, label.y.npc= .9, color="red") +
  scale_fill_manual(values=c("salmon", "steelblue"))
#scale_fill_manual(values=c("orange", "darkgreen"))