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library(tidyverse)
library(ggplot2)
library(ggpubr)#Read in sequencing count data

LRIIIReads <- read.table("/Volumes/Macintosh HD/Users/gregg/Downloads/LRIII.txt",

                         header=FALSE, stringsAsFactors = FALSE, na.strings = "")

#adjust names back to simple sample names

LRIIIReads <- separate(LRIIIReads, 2, sep="[.]", into = c(NA, "samplename", NA, NA, NA, NA, NA, NA, NA))

#remove the total line and rename columns

LRIIIReads <- LRIIIReads[(1:144),]

colnames(LRIIIReads) <- c("readsx4", "samplename")

#Divide read count by 4 to get the proper number

LRIIIReads$readsk <- LRIIIReads$readsx4 / 4

#Add the replicates together

LRIIIReads <- LRIIIReads %>%

  group_by(samplename) %>%

  summarise(reads = sum(readsk))

#read in the qPCR data, subset columns to sample name, mean qty, and standard deviation

DGqPCR <- read.csv("/Volumes/Macintosh HD/Users/gregg/Downloads/5DG5_COL456.csv",

                   header=TRUE, stringsAsFactors = FALSE, na.strings = "", skip =14 )

DGqPCR <- DGqPCR[ , c(2, 8, 9)]

DGqPCR$plate <- "5DG5"

LVDqPCR <- read.csv("/Volumes/Macintosh HD/Users/gregg/Downloads/5LVD5_Col123.csv",

                    header=TRUE, stringsAsFactors = FALSE, na.strings = "", skip =14 )

LVDqPCR <- LVDqPCR[ , c(2, 8, 9)]

LVDqPCR$plate <- "5LVD5"

MCqPCR <- read.csv("/Volumes/Macintosh HD/Users/gregg/Downloads/MC_MB_Comparison.csv",

                   header=TRUE, stringsAsFactors = FALSE, na.strings = "", skip =14 )

MCqPCR <- MCqPCR[ , c(2, 8, 9)]

MCqPCR$plate <- "MC"

#adjust to match naming conventionsbetween files

MCqPCR[,1] <- gsub("MC_A", "MCA_", MCqPCR[,1])

MCqPCR[,1] <- gsub("MC_B", "MCB_", MCqPCR[,1])

MCqPCR[,1] <- gsub("MC_C", "MCC_", MCqPCR[,1])

MCqPCR[,1] <- gsub("MC_D", "MCD_", MCqPCR[,1])

#combine data

qPCR <- rbind(DGqPCR, LVDqPCR, MCqPCR)

#reduce to one incidence of each sample

qPCR <- qPCR %>%

  group_by(Sample.Name) %>%

  slice(1)

colnames(qPCR) <- c("samplename", "mean", "stddev", "plate")

#combine qPCR and read data together

LRIIIReads <- left_join(LRIIIReads, qPCR, by = "samplename")

#plot reads vs qPCR qty mean

ggplot(LRIIIReads, aes(readsmean, meanreads, color=plate, shape=plate))+
   geom_point(show.legend = TRUE)+
   geom_errorbar(aes(yminxmin=mean-stddev, ymaxxmax=mean+stddev), width=.2)+
   geom_smooth(method='lm', formula= y~x)+
   stat_regline_equation(label.y = 250200000, aes(label = ..eq.label..)) +
   stat_regline_equation(label.y = 150150000, aes(label = ..rr.label..))+
   facet_wrap(~plate)