library(ggplot2)
library(cowplot)
library(scales)
library(gridExtra)
library(grid)
library(ggplotify)
library(dplyr)
library(data.table)
dat<-fread('output/statsFiles/tmp/ONT_Pre_0+.LiverRep1.readlength.tsv.gz', header=T, sep='\t')
dat <- subset(dat, seqTech=='ONT')

dat <- subset(dat, capDesign=='Pre')


dat <- subset(dat, sizeFrac=='0+')

dat <- subset(dat, sampleRep=='LiverRep1')


dat$seqTech <- gsub('-', '\n', dat$seqTech)

dat$sampleRep <- gsub('Pre_', '', dat$sampleRep)



horizCats <- length(unique(dat$capDesign)) * length(unique(dat$sampleRep))
vertCats <- length(unique(dat$seqTech))

wXyPlot = (horizCats * 0.9) +1.7
hXyPlot = (vertCats * 0.6) + 1.7

geom_textSize=1.4 
themeSize = (14/5) * geom_textSize
# https://stackoverflow.com/questions/25061822/ggplot-geom-text-font-size-control/25062509
lineSize=geom_textSize/8
minorLineSize=lineSize/2



wXyPlot = wXyPlot * 1.2

dat$sizeFrac_f=factor(dat$sizeFrac, levels=names(c('0+'='#b3b3b3', '0-1' ='#f765ac','1+' ='#b370f9')), ordered=TRUE)
dat %>%
  group_by(seqTech, sizeFrac_f, capDesign, sampleRep) %>%
  summarise(n=n(), med=median(length)) -> datSumm


summaryStats = transform(datSumm, LabelN = paste0('N= ', comma(n)), LabelM = paste0( 'Median= ', comma(med))) 

plotBase <- "p <- ggplot(dat, aes(x=length)) +
geom_histogram(aes(y=..density..,fill=sizeFrac_f), binwidth=100) +
geom_vline(data = summaryStats, aes(xintercept=med), color='#ff0055', linetype='solid', size=lineSize) +
scale_fill_manual(values=c('0+'='#b3b3b3', '0-1' ='#f765ac','1+' ='#b370f9')) +
geom_text(data = summaryStats, aes(label = LabelN, x = Inf, y = Inf), hjust=1, vjust=1,  size=geom_textSize, fontface = 'bold') +
geom_text(data = summaryStats, aes(label = LabelM, x = med, y = Inf), hjust=-0.1, vjust=2.5,  size=geom_textSize, fontface = 'bold', color='#ff0055') +
coord_cartesian(xlim=c(0, 3500)) +
#scale_y_continuous(labels=scientific)+
scale_x_continuous(labels=comma, name='Read length (nts)')+
theme(axis.text= element_text(size=themeSize*1.8), axis.ticks = element_line(size=lineSize), axis.line = element_line(colour = '#595959', size=lineSize), axis.title=element_text(size = themeSize*2), panel.grid.major = element_line(colour='#d9d9d9', size=lineSize),panel.grid.minor = element_line(colour='#e6e6e6', size=minorLineSize),panel.border = element_blank(),panel.background = element_blank(), strip.background = element_rect(colour='#737373',fill='white'), legend.key.size=unit(0.5,'line'), legend.title=element_text(size=themeSize*1.2), legend.text=element_text(size=themeSize), strip.text = element_text(size = themeSize)) + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + "


plotFacetXy <- parse(text =paste(plotBase, "facet_grid( seqTech ~ capDesign + sampleRep, scales='free_y')"))
plotFacetYx <- parse(text=paste(plotBase, "facet_grid( capDesign + sampleRep ~ seqTech, scales='free_y')"))

plotFacetXy <- parse(text =paste(plotFacetXy, " + theme(strip.text.x = element_blank(), strip.text.y = element_blank())"))
plotFacetYx <- parse(text=paste(plotFacetYx, " + theme(strip.text.x = element_blank(), strip.text.y = element_blank())"))

pXy <- eval(plotFacetXy)
pYx <- eval(plotFacetYx)

legend <- get_legend(pXy)

pXyNoLegend <- pXy + theme(legend.position='none')
pYxNoLegend <- pYx + theme(legend.position='none')

legendOnly <- grid.arrange(legend)
pXyGrob <- as.grob(pXy)
pYxGrob <- as.grob(pYx)
pXyNoLegendGrob <- as.grob(pXyNoLegend)
pYxNoLegendGrob <- as.grob(pYxNoLegend)


hLegendOnly <- convertUnit(sum(legend$heights), 'in', valueOnly=TRUE)
wLegendOnly <- convertUnit(sum(legend$widths), 'in', valueOnly=TRUE)


hYxPlot <- wXyPlot
wYxPlot <- hXyPlot 

hXyNoLegendPlot<- hXyPlot 
wXyNoLegendPlot<- wXyPlot - wLegendOnly

hYxNoLegendPlot<- hYxPlot
wYxNoLegendPlot<- wYxPlot - wLegendOnly


wYxPlot = wYxPlot * 1.2
wYxNoLegendPlot<- wYxPlot - wLegendOnly

save_plot('output/plots/readLength.stats/ONT/Pre/ONT_Pre_0+_LiverRep1.readLength.stats.legendOnly.png', legendOnly, base_width=wLegendOnly, base_height=hLegendOnly)
save_plot('output/plots/readLength.stats/ONT/Pre/ONT_Pre_0+_LiverRep1.readLength.stats.xy.wLegend.png', pXy, base_width=wXyPlot, base_height=hXyPlot)

save_plot('output/plots/readLength.stats/ONT/Pre/ONT_Pre_0+_LiverRep1.readLength.stats.xy.woLegend.png', pXyNoLegend, base_width=wXyNoLegendPlot, base_height=hXyNoLegendPlot)
save_plot('output/plots/readLength.stats/ONT/Pre/ONT_Pre_0+_LiverRep1.readLength.stats.yx.wLegend.png', pYx, base_width=wYxPlot, base_height=hYxPlot)

save_plot('output/plots/readLength.stats/ONT/Pre/ONT_Pre_0+_LiverRep1.readLength.stats.yx.woLegend.png', pYxNoLegend, base_width=wYxNoLegendPlot, base_height=hYxNoLegendPlot)