document.write('
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  1. #Assay plot beta script
  2.  
  3. library(ggplot2)
  4. library(reshape2)
  5. data=read.csv(file.choose(), header = F, dec = ",", sep = ";")
  6. data_s<-t(data)
  7. data_s<-as.numeric(data_s) #linearisiert die matrix
  8. #rows anpassen
  9. data_s<-matrix(data_s,ncol = 51,nrow = 201) #struktur der matrix wiederherstellen
  10. data_s = data_s[-1,]
  11.  
  12. #blank einlesen
  13. blank=read.csv(file.choose(), header = F, dec = ",", sep = ";")
  14. blank_s<-t(blank)
  15. blank_s<-as.numeric(blank_s) #linearisiert die matrix
  16. #rows anpassen
  17. blank_s<-matrix(blank_s,ncol = 5,nrow = 7) #struktur der matrix wiederherstellen
  18. blank_s = blank_s[-1,]
  19.  
  20.  
  21. b_small <- blank_s[,c(1,4,5)]
  22. b_smalld <- as.data.frame(b_small)
  23. colnames(b_smalld) <- c("well","A","B")
  24. b_melt = melt(b_smalld, id="well")
  25.  
  26. #obere reihe    16-21 / 28-33 / 40-45
  27. for (i in 1:6) {
  28.   d_small <- data_s[,c(1,15+i,27+i,39+i)]
  29.   #d_small <- data_s[,c(1,17,29,41)]
  30.   d_smalld <- as.data.frame(d_small)
  31.   colnames(d_smalld) <- c("kc","p","ca","k")
  32.   d_melt = melt(d_smalld, id="kc")
  33.  
  34.  
  35.   colnames(d_melt) <- c("kc","samples","value")
  36.  
  37.   #d_melt[,3]=d_melt[,3]-b_melt[2,3]  
  38.    
  39.   p <- ggplot(d_melt) + geom_line(aes(x=kc, y=value, colour=samples)) +
  40.     scale_colour_manual(values=c("red","green","blue")) + theme(legend.position="top") +  xlab("kinetic cycles") + ylab("A620")
  41.   #paste anpassen "LETTER i.e. e/f/..."
  42.  
  43.   #ggsave(file = paste("e2_blank.png", sep = ""), path = "/Users/Steven/Seafile/iGEM 2015/Labor/ItaXyl/AssayStuff/Auswertung/",width = 7, height = 6, dpi = 300)
  44.   ggsave(file = paste("e",i,".png", sep = ""), path = "/Users/Steven/Seafile/iGEM 2015/Labor/ItaXyl/AssayStuff/Auswertung/",width = 7, height = 6, dpi = 300)
  45. }
  46.  
  47. #untere reihe   22-27 / 34-39 / 46-51
  48. for (i in 1:6) {
  49.   d_small <- data_s[,c(1,21+i,33+i,45+i)]
  50.   #d_small <- data_s[,c(1,22,34,46)]
  51.   d_smalld <- as.data.frame(d_small)
  52.   colnames(d_smalld) <- c("kc","p","ca","k")
  53.   d_melt = melt(d_smalld, id="kc")
  54.  
  55.   colnames(d_melt) <- c("kc","samples","value")
  56.  
  57.   #d_melt[,3]=d_melt[,3]-b_melt[6+i,3]  
  58.  
  59.   p <- ggplot(d_melt) + geom_line(aes(x=kc, y=value, colour=samples)) +
  60.     scale_colour_manual(values=c("red","green","blue")) + theme(legend.position="top") +  xlab("kinetic cycles") + ylab("A620")
  61. #paste anpassen "LETTER i.e. e/f/..."
  62.   ggsave(file = paste("f",i,".png", sep = ""), path = "/Users/Steven/Seafile/iGEM 2015/Labor/ItaXyl/AssayStuff/Auswertung/",width = 7, height = 6, dpi = 300)
  63. }
  64.  
  65.  
  66. #DER GROSSE UMSORTIERER
  67. #d_p  = melt(d_smalld, id="kc")
  68. #d_p <- d_p[-c(101:300),]
  69. #d_ca = melt(d_smalld, id="kc")
  70. #d_ca <- d_ca[-c(1:100),]
  71. #rownames(d_ca) <- 1:nrow(d_ca)
  72. #d_ca <- d_ca[-c(101:200),]
  73. #colnames(d_ca) <- c("kc","variable2","value2")
  74. #d_k  = melt(d_smalld, id="kc")
  75. #d_k <- d_k[-c(1:200),]
  76. #rownames(d_k) <- 1:nrow(d_k)
  77. #colnames(d_k)  <- c("kc","variable3","value3")
  78. #d_partly <- merge(d_p,d_ca)
  79. #d_whole <- merge(d_partly,d_k)
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