#Assay plot beta script
library(ggplot2)
library(reshape2)
data=read.csv(file.choose(), header = F, dec = ",", sep = ";")
data_s<-t(data)
data_s<-as.numeric(data_s) #linearisiert die matrix
#rows anpassen
data_s<-matrix(data_s,ncol = 51,nrow = 201) #struktur der matrix wiederherstellen
data_s = data_s[-1,]
#blank einlesen
blank=read.csv(file.choose(), header = F, dec = ",", sep = ";")
blank_s<-t(blank)
blank_s<-as.numeric(blank_s) #linearisiert die matrix
#rows anpassen
blank_s<-matrix(blank_s,ncol = 5,nrow = 7) #struktur der matrix wiederherstellen
blank_s = blank_s[-1,]
b_small <- blank_s[,c(1,4,5)]
b_smalld <- as.data.frame(b_small)
colnames(b_smalld) <- c("well","A","B")
b_melt = melt(b_smalld, id="well")
#obere reihe 16-21 / 28-33 / 40-45
for (i in 1:6) {
d_small <- data_s[,c(1,15+i,27+i,39+i)]
#d_small <- data_s[,c(1,17,29,41)]
d_smalld <- as.data.frame(d_small)
colnames(d_smalld) <- c("kc","p","ca","k")
d_melt = melt(d_smalld, id="kc")
colnames(d_melt) <- c("kc","samples","value")
#d_melt[,3]=d_melt[,3]-b_melt[2,3]
p <- ggplot(d_melt) + geom_line(aes(x=kc, y=value, colour=samples)) +
scale_colour_manual(values=c("red","green","blue")) + theme(legend.position="top") + xlab("kinetic cycles") + ylab("A620")
#paste anpassen "LETTER i.e. e/f/..."
#ggsave(file = paste("e2_blank.png", sep = ""), path = "/Users/Steven/Seafile/iGEM 2015/Labor/ItaXyl/AssayStuff/Auswertung/",width = 7, height = 6, dpi = 300)
ggsave(file = paste("e",i,".png", sep = ""), path = "/Users/Steven/Seafile/iGEM 2015/Labor/ItaXyl/AssayStuff/Auswertung/",width = 7, height = 6, dpi = 300)
}
#untere reihe 22-27 / 34-39 / 46-51
for (i in 1:6) {
d_small <- data_s[,c(1,21+i,33+i,45+i)]
#d_small <- data_s[,c(1,22,34,46)]
d_smalld <- as.data.frame(d_small)
colnames(d_smalld) <- c("kc","p","ca","k")
d_melt = melt(d_smalld, id="kc")
colnames(d_melt) <- c("kc","samples","value")
#d_melt[,3]=d_melt[,3]-b_melt[6+i,3]
p <- ggplot(d_melt) + geom_line(aes(x=kc, y=value, colour=samples)) +
scale_colour_manual(values=c("red","green","blue")) + theme(legend.position="top") + xlab("kinetic cycles") + ylab("A620")
#paste anpassen "LETTER i.e. e/f/..."
ggsave(file = paste("f",i,".png", sep = ""), path = "/Users/Steven/Seafile/iGEM 2015/Labor/ItaXyl/AssayStuff/Auswertung/",width = 7, height = 6, dpi = 300)
}
#DER GROSSE UMSORTIERER
#d_p = melt(d_smalld, id="kc")
#d_p <- d_p[-c(101:300),]
#d_ca = melt(d_smalld, id="kc")
#d_ca <- d_ca[-c(1:100),]
#rownames(d_ca) <- 1:nrow(d_ca)
#d_ca <- d_ca[-c(101:200),]
#colnames(d_ca) <- c("kc","variable2","value2")
#d_k = melt(d_smalld, id="kc")
#d_k <- d_k[-c(1:200),]
#rownames(d_k) <- 1:nrow(d_k)
#colnames(d_k) <- c("kc","variable3","value3")
#d_partly <- merge(d_p,d_ca)
#d_whole <- merge(d_partly,d_k)