comparison RScript.r @ 70:9643b1fd9c45 draft default tip

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69:c532b3f8dc97

      p = NULL
      print(paste("nrow scatterplot_locus_data", nrow(scatterplot_locus_data)))
      if(nrow(scatterplot_locus_data) != 0){
        if(on == "normalized_read_count"){
          scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
          p = ggplot(scatterplot_locus_data, aes(factor(reorder(type, type.order)), normalized_read_count, group=link)) + geom_line() + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,10^6)) + scale_x_discrete(breaks=levels(scatterplot_data$type), labels=levels(scatterplot_data$type), drop=FALSE)
        } else {
          p = ggplot(scatterplot_locus_data, aes(factor(reorder(type, type.order)), Frequency, group=link)) + geom_line() + scale_y_log10(limits=c(0.0001,100), breaks=c(0.0001, 0.001, 0.01, 0.1, 1, 10, 100), labels=c("0.0001", "0.001", "0.01", "0.1", "1", "10", "100")) + scale_x_discrete(breaks=levels(scatterplot_data$type), labels=levels(scatterplot_data$type), drop=FALSE)
        }
        p = p + geom_point(aes(colour=type), position="dodge")
        p = p + xlab("In one or both samples") + ylab(onShort) + ggtitle(paste(patient1[1,patientIndex], patient1[1,sampleIndex], patient2[1,sampleIndex], onShort, product[iter, titleIndex]))

      if(sum(in_three)> 0){
				scatterplot_locus_data[in_three,]$type = "In three"
      }
      not_in_one = scatterplot_locus_data$type != "In one"
      if(sum(not_in_one) > 0){
				scatterplot_locus_data[not_in_one,]$type = "In multiple"
      }
      p = NULL
      if(nrow(scatterplot_locus_data) != 0){
        if(on == "normalized_read_count"){
					scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
          p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,1000000))
        } else {
          p = ggplot(scatterplot_locus_data, aes(type, Frequency)) + scale_y_log10(limits=c(0.0001,100), breaks=c(0.0001, 0.001, 0.01, 0.1, 1, 10, 100), labels=c("0.0001", "0.001", "0.01", "0.1", "1", "10", "100")) + expand_limits(y=c(0,100))
          #p = ggplot(scatterplot_locus_data, aes(type, Frequency)) + scale_y_continuous(limits = c(0, 100)) + expand_limits(y=c(0,100))
        }

  png(paste(label1, "_", label2, "_", label3, "_", onShort, "_indiv_all.png", sep=""), width=1920, height=1080)
  print(plt)
  dev.off()
}

if(F & nrow(triplets) != 0){

  cat("<tr><td>Starting triplet analysis</td></tr>", file=logfile, append=T)

  triplets$uniqueID = "ID"
  

70:9643b1fd9c45

      p = NULL
      print(paste("nrow scatterplot_locus_data", nrow(scatterplot_locus_data)))
      if(nrow(scatterplot_locus_data) != 0){
        if(on == "normalized_read_count"){
          scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
          #p = ggplot(scatterplot_locus_data, aes(factor(reorder(type, type.order)), normalized_read_count, group=link)) + geom_line() + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,10^6)) + scale_x_discrete(breaks=levels(scatterplot_data$type), labels=levels(scatterplot_data$type), drop=FALSE)
          print(paste("scatterplot_locus_data:"))
          print(head(scatterplot_locus_data))
          p = ggplot(scatterplot_locus_data, aes(factor(reorder(type, type.order)), normalized_read_count, group=link)) + geom_line() + scale_y_log10(breaks=scales,labels=scales, limits=c(0,10^6)) + scale_x_discrete(breaks=levels(scatterplot_data$type), labels=levels(scatterplot_data$type), drop=FALSE)
        } else {
          p = ggplot(scatterplot_locus_data, aes(factor(reorder(type, type.order)), Frequency, group=link)) + geom_line() + scale_y_log10(limits=c(0.0001,100), breaks=c(0.0001, 0.001, 0.01, 0.1, 1, 10, 100), labels=c("0.0001", "0.001", "0.01", "0.1", "1", "10", "100")) + scale_x_discrete(breaks=levels(scatterplot_data$type), labels=levels(scatterplot_data$type), drop=FALSE)
        }
        p = p + geom_point(aes(colour=type), position="dodge")
        p = p + xlab("In one or both samples") + ylab(onShort) + ggtitle(paste(patient1[1,patientIndex], patient1[1,sampleIndex], patient2[1,sampleIndex], onShort, product[iter, titleIndex]))

      if(sum(in_three)> 0){
				scatterplot_locus_data[in_three,]$type = "In three"
      }
      not_in_one = scatterplot_locus_data$type != "In one"
      if(sum(not_in_one) > 0){
				#scatterplot_locus_data[not_in_one,]$type = "In multiple"
      }
      p = NULL
      if(nrow(scatterplot_locus_data) != 0){
        if(on == "normalized_read_count"){
		  scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
          p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,1000000))
        } else {
          p = ggplot(scatterplot_locus_data, aes(type, Frequency)) + scale_y_log10(limits=c(0.0001,100), breaks=c(0.0001, 0.001, 0.01, 0.1, 1, 10, 100), labels=c("0.0001", "0.001", "0.01", "0.1", "1", "10", "100")) + expand_limits(y=c(0,100))
          #p = ggplot(scatterplot_locus_data, aes(type, Frequency)) + scale_y_continuous(limits = c(0, 100)) + expand_limits(y=c(0,100))
        }

  png(paste(label1, "_", label2, "_", label3, "_", onShort, "_indiv_all.png", sep=""), width=1920, height=1080)
  print(plt)
  dev.off()
}

if(nrow(triplets) != 0){

  cat("<tr><td>Starting triplet analysis</td></tr>", file=logfile, append=T)

  triplets$uniqueID = "ID"