compile.Rmd

---
title: "compile plate reader data"
author: "Cameron Strachan"
date: "August 4, 2016"
output: html_document
---

```{r}
library(reshape2)
library(ggplot2)
library(gridExtra)
library(RColorBrewer)
library(tidyr)

print("loading compile_inputs.csv from the current working directory")
getwd()

INPUTS <- read.csv("compile_inputs.csv")
inputfiles <- INPUTS[,1]=="File" 
datfilenames<- INPUTS[inputfiles,2] # the list of inputs that are data files to be loaded
datfilenames<- unique(datfilenames) # remove duplicates (mistakes)
DAT<- read.csv(as.character(datfilenames[1]))
head(data)
```

```{r}
plates <- 25*100*2
i <- seq(29, plates, by = 58)
j <- seq(48, plates, by = 58)


fu85 <- DAT[i,]
fu85 <- na.omit(fu85) # remove NA values
fu85 <- as.data.frame(fu85) #check to make sure its a data frame


fu90 <- DAT[j,]
fu90 <- na.omit(fu90)
fu90 <- as.data.frame(fu90)
```

```{r}
names <-DAT[22,]
names[,1] <- list(NULL)
colnames = as.character(unlist(names[1,]))
colnames(fu85)[2:ncol(fu85)] <- colnames
colnames(fu85)[1] <- c("Plate")



write.csv(fu85, "~/Desktop/170119 hep 5mM od compiled.csv")
write.csv(fu90, "~/Desktop/170119 hep 5mM gfp compiled.csv")

data <- read.csv("~/Desktop/160902_Screen_Comp.csv")

d_fu <- fu
d_fu <- separate(d_fu, col = Plate, into = c("Plate", "Treatment"), sep = "\\(")
d_fu <- separate(d_fu, col = Treatment, into = c("Treatment", "rm", sep = "\\)"))
d_fu[,c(3,4)] <- list(NULL)




data$Treatment[c(4,9)] <- "e"

eth <- subset(data, data$Treatment == "e")
bis <- subset(data, data$Treatment == "b")
pim <- subset(data, data$Treatment == "p")
hep <- subset(data, data$Treatment == "h")
wat <- subset(data, data$Treatment == "water")

bis_fold <- bis / 

write.csv(d_fu, "~/Desktop/161007_7aminoheptanoic_MM.csv")
write.csv(d_od, "~/Desktop/161005_hep_od6.csv")



```