comparison RScript.r @ 32:dde5ec847549 draft

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31:ce8bd23d0335

lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="normalized_read_count")

cat("</table></html>", file=logfile, append=T)

scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
p = ggplot(single_patients, aes(Rearrangement, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales)
p = p + geom_point(aes(colour=type), position="jitter")
p = p + xlab("In one or both samples") + ylab("Reads")
p = p + facet_grid(.~Patient) + ggtitle("Scatterplot of the reads of the patients with a single sample")
png("singles_reads_scatterplot.png", width=640 * length(unique(single_patients$Patient)), height=1080)
print(p)
dev.off()

p = ggplot(single_patients, aes(Rearrangement, Frequency))
p = p + geom_point(aes(colour=type), position="jitter")
p = p + xlab("In one or both samples") + ylab("Frequency")
p = p + facet_grid(.~Patient) + ggtitle("Scatterplot of the frequency of the patients with a single sample")
png("singles_freq_scatterplot.png", width=640 * length(unique(single_patients$Patient)), height=1080)
print(p)

      }
      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)
        } else {
          p = ggplot(scatterplot_locus_data, aes(type, Frequency)) 
        }
        p = p + geom_point(aes(colour=type), position="jitter")
        p = p + xlab("In one or in multiple samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))
      } else {
        p = ggplot(NULL, aes(x=c("In one", "In multiple"),y=0)) + geom_blank(NULL) + xlab("In two or in three of the samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))

32:dde5ec847549

lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="normalized_read_count")

cat("</table></html>", file=logfile, append=T)

scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
p = ggplot(single_patients, aes(Rearrangement, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,1000000))
p = p + geom_point(aes(colour=type), position="jitter")
p = p + xlab("In one or both samples") + ylab("Reads")
p = p + facet_grid(.~Patient) + ggtitle("Scatterplot of the reads of the patients with a single sample")
png("singles_reads_scatterplot.png", width=640 * length(unique(single_patients$Patient)), height=1080)
print(p)
dev.off()

p = ggplot(single_patients, aes(Rearrangement, Frequency)) + scale_y_continuous(limits = c(0, 100)) + expand_limits(y=c(0,100))
p = p + geom_point(aes(colour=type), position="jitter")
p = p + xlab("In one or both samples") + ylab("Frequency")
p = p + facet_grid(.~Patient) + ggtitle("Scatterplot of the frequency of the patients with a single sample")
png("singles_freq_scatterplot.png", width=640 * length(unique(single_patients$Patient)), height=1080)
print(p)

      }
      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_continuous(limits = c(0, 100)) + expand_limits(y=c(0,100))
        }
        p = p + geom_point(aes(colour=type), position="jitter")
        p = p + xlab("In one or in multiple samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))
      } else {
        p = ggplot(NULL, aes(x=c("In one", "In multiple"),y=0)) + geom_blank(NULL) + xlab("In two or in three of the samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))