params <- list(alignments = "/tmp/Rtmp4Rz0VV/Rinst3c412843f4538d/amplican/extdata/results/alignments/events_filtered_shifted_normalized.csv", config_summary = "/tmp/Rtmp4Rz0VV/Rinst3c412843f4538d/amplican/extdata/results/config_summary.csv", unassigned_folder = "/tmp/Rtmp4Rz0VV/Rinst3c412843f4538d/amplican/extdata/results/alignments/unassigned_reads.csv", top = 5L) ## ----load data, message=F, warning=FALSE, include=FALSE----------------------- library(amplican) library(ggplot2) alignments <- data.table::fread(params$alignments) data.table::setDF(alignments) config <- data.frame(data.table::fread(params$config_summary)) height <- amplican::plot_height(length(unique(config$Barcode))) ## ----group ids, echo=FALSE, message=F, warning=FALSE-------------------------- library(knitr) groupDF <- data.frame(group = unique(config$Barcode), IDs = sapply(unique(config$Barcode), function(x) toString(config$ID[config$Barcode == x]))) kable(groupDF, row.names = FALSE) ## ----plot_total_reads, echo=FALSE, fig.height=height + height/4, fig.width=14, message=F, warning=FALSE---- p <- ggplot(data = config, aes(x = as.factor(Barcode), y = log10(Reads + 1), order = Barcode, fill = ID)) + geom_bar(position='stack', stat='identity') + ylab('Number of reads + 1, log10 scaled') + xlab('Barcode') if (length(groupDF$group) > 20) { p <- p + theme(legend.position = 'none', legend.direction = 'horizontal', axis.text = element_text(size = 12), axis.title = element_text(size = 14, face = 'bold')) } else { p <- p + theme(legend.position = 'top', legend.direction = 'horizontal', axis.text = element_text(size = 12), axis.title = element_text(size = 14, face = 'bold'), legend.title = element_blank()) } p + coord_flip() ## ----plot_filter_per, echo=FALSE, fig.height=height, fig.width=14, message=F, warning=FALSE---- barcodeTable <- aggregate(cbind(Reads, Reads_Filtered, PRIMER_DIMER, Low_Score, Reads_Edited, Reads_Frameshifted) ~ Barcode, data = config, sum) barcodeTable$F_percentage <- (barcodeTable$PRIMER_DIMER + barcodeTable$Low_Score) * 100/barcodeTable$Reads barcodeTable$F_percentage[is.nan(barcodeTable$F_percentage)] <- 0 ggplot(data = barcodeTable, aes(x = as.factor(Barcode), y = F_percentage, order = Barcode, fill = Barcode)) + geom_bar(stat='identity') + ylab('Percentage of filtered reads') + xlab('Barcode') + theme(axis.text = element_text(size=12), axis.title = element_text(size=14, face = 'bold'), legend.position = 'none') + ylim(0, 100) + coord_flip() ## ----plot mut percentage, echo=FALSE, fig.height=height,fig.width=14, message=F, warning=FALSE---- barcodeTable$edit_percentage <- barcodeTable$Reads_Edited * 100/barcodeTable$Reads_Filtered barcodeTable$edit_percentage[is.nan(barcodeTable$edit_percentage)] <- 0 ggplot(data = barcodeTable, aes(x = as.factor(Barcode), y = edit_percentage, order = Barcode)) + geom_bar(stat = 'identity') + ylab('Percentage of reads (not filtered) that have edits') + theme(axis.text = element_text(size=12), axis.title = element_text(size=14, face = 'bold')) + ylim(0,100) + xlab('Barcode') + coord_flip() + geom_text(aes(x = as.factor(Barcode), y = edit_percentage, label = Reads_Edited), hjust = -1) ## ----plot_frameshift_per, echo=FALSE, fig.height=height, fig.width=14, message=F, warning=FALSE---- barcodeTable$frameshift_percentage <- barcodeTable$Reads_Frameshifted * 100/barcodeTable$Reads_Filtered barcodeTable$frameshift_percentage[is.nan(barcodeTable$frameshift_percentage)] <- 0 ggplot(data = barcodeTable, aes(x = as.factor(Barcode), y = frameshift_percentage, order = Barcode)) + geom_bar(position = 'stack', stat = 'identity') + ylab('Percentage of reads (not filtered) that have frameshift') + xlab('Barcode') + theme(axis.text = element_text(size=12), axis.title = element_text(size=14,face = 'bold')) + ylim(0, 100) + coord_flip() + geom_text(aes(x = as.factor(Barcode), y = frameshift_percentage, label = Reads_Frameshifted), hjust = -1) ## ----plot read heterogeneity, echo=FALSE, fig.height=height + 1, fig.width=14, message=F, warning=FALSE---- plot_heterogeneity(alignments, config, level = 'Barcode') ## ----plot read unassigned reads, results = "asis", echo=FALSE, message=F, warning=FALSE, comment = ''---- if (file.exists(params$unassigned_folder) && !any(is.na(config$Forward_Reads_File)) && !any(is.na(config$Reverse_Reads_File))) { unassigned_reads <- data.table::fread(params$unassigned_folder) data.table::setDF(unassigned_reads) cat("# Top unassigned reads \n\n*** \n\n") for (b in unique(unassigned_reads$Barcode)) { cat("## ", b, " \n\n", sep = "") b_unassiged <- unassigned_reads[unassigned_reads$Barcode == b, ] b_unassiged <- b_unassiged[order(b_unassiged$BarcodeFrequency, decreasing = TRUE), ] if (dim(b_unassiged)[1] == 0) { cat(knitr::asis_output("No unassigned reads in this barcode. That\'s great! \n\n")) } else { topN <- if (dim(b_unassiged)[1] < params$top) dim(b_unassiged)[1] else params$top cat('\n') print(knitr::kable(data.frame(Forward = paste0('P', 1:topN), Reverse = paste0('S', 1:topN), Counts = b_unassiged[1:topN, 'Total'], Frequency = b_unassiged[1:topN, 'BarcodeFrequency']))) cat("\n") cat("
", paste(amplican_print_reads(b_unassiged[1:topN, 'Forward'],
                                              b_unassiged[1:topN, 'Reverse']),
                         collapse = "\n"), "
") cat("\n\n") } } }