params <- list(barcode_summary = "/tmp/RtmpqwloUY/Rinst679e2d50f213/amplican/extdata/results/barcode_reads_filters.csv", config_summary = "/tmp/RtmpqwloUY/Rinst679e2d50f213/amplican/extdata/results/config_summary.csv", links = "1. [Report by id](./example_id_report.html)\n2. [Report by barcode](./example_barcode_report.html)\n3. [Report by group](./example_group_report.html)\n4. [Report by guide](./example_guide_report.html)\n5. [Report by amplicon](./example_amplicon_report.html)\n") ## ----echo = F, results = 'asis'----------------------------------------------- if (params$links != "") { cat("***\n") cat("# Other Reports\n") cat("***\n") cat(params$links, sep = "") } ## ----echo = F----------------------------------------------------------------- library(ggplot2) library(waffle) summaryDF <- data.frame(data.table::fread(params$barcode_summary)) total_reads <- sum(summaryDF$read_count) total_good_reads <- sum(summaryDF$filtered_read_count) read_q <- c(total_good_reads, total_reads - total_good_reads) read_q_per <- round(read_q*100/total_reads) read_q_per[is.na(read_q_per)] <- 0 # For some cases 0/0 happens, yelding NaN names(read_q_per) <- c(paste0('Good Reads\n', read_q[1], ' (', read_q_per[1], '%)'), paste0('Bad Quality Reads\n', read_q[2], ' (', read_q_per[2], '%)')) waffle(read_q_per, legend_pos = 'bottom', title = "Quality of all reads", rows = 10, colors = c('#E69F00', '#000000')) bad_read_q <- c(sum(summaryDF$bad_base_quality), sum(summaryDF$bad_average_quality), sum(summaryDF$bad_alphabet)) bad_read_q_per <- round(bad_read_q*100/sum(bad_read_q)) bad_read_q_per[is.na(bad_read_q_per)] <- 0 names(bad_read_q_per) <- c( paste0('Bad Base Quality\n', bad_read_q[1], ' (', bad_read_q_per[1], '%)'), paste0('Bad Average Read Quality\n', bad_read_q[2], ' (', bad_read_q_per[2], '%)'), paste0('Bad Read Alphabet\n', bad_read_q[3], ' (', bad_read_q_per[3], '%)')) waffle(bad_read_q_per, legend_pos = 'bottom', title = "\n\nBad quality reads", rows = 10, colors = c('#D55e00', '#f0e442', '#009e73')) ## ----echo = F----------------------------------------------------------------- # Assignment of reads from barcodes into experiments (ID) total_ureads <- sum(summaryDF$unique_reads) read_a <- c(sum(summaryDF$assigned_reads), sum(summaryDF$unassigned_reads)) read_a_per <- round(read_a*100/total_ureads) read_a_per[is.na(read_a_per)] <- 0 names(read_a_per) <- c(paste0('Assigned Reads\n', read_a[1], ' (', read_a_per[1], '%)'), paste0('Unassigned Reads\n', read_a[2], ' (', read_a_per[2], '%)')) waffle(read_a_per, legend_pos = 'bottom', title = "Succesfull assignment of unique reads", rows = 10, colors = c('#E69F00', '#000000')) # Filtered reads configDF <- data.frame(data.table::fread(params$config_summary)) height <- amplican::plot_height(length(unique(configDF$Barcode))) F_reads <- c(sum(configDF$Reads_Filtered), sum(configDF$PRIMER_DIMER), sum(configDF$Low_Score)) F_reads_per <- round(F_reads*100/sum(configDF$Reads)) F_reads_per[is.na(F_reads_per)] <- 0 names(F_reads_per) <- c(paste0('Good Reads\n', F_reads[1], ' (', F_reads_per[1], '%)'), paste0('PRIMER DIMERs\n', F_reads[2], ' (', F_reads_per[2], '%)'), paste0('Low Score\n', F_reads[3], ' (', F_reads_per[3], '%)')) waffle(F_reads_per, legend_pos = 'bottom', title = "\n\nFiltered Reads", rows = 10, colors = c('#E69F00', '#000000', '#A9A9A9')) ## ----echo = F----------------------------------------------------------------- total_reads <- sum(configDF$Reads_Filtered) total_reads_ctr <- sum(configDF$Reads_Filtered[configDF$Control]) total_reads_tmt <- sum(configDF$Reads_Filtered[!configDF$Control]) reads_edited <- c(sum(configDF$Reads_Edited[!configDF$Control]), # Treatment total_reads_tmt - sum(configDF$Reads_Edited[!configDF$Control]), sum(configDF$Reads_Edited[configDF$Control]), # Control total_reads_ctr - sum(configDF$Reads_Edited[configDF$Control])) reads_edited_per <- round(reads_edited*100/total_reads) reads_edited_per[is.na(reads_edited_per)] <- 0 names(reads_edited_per) <- c( paste0('Edits in Treatment\n', reads_edited[1], ' (', reads_edited_per[1], '%)'), paste0('No Edits in Treatment\n', reads_edited[2], ' (', reads_edited_per[2], '%)'), paste0('Edits in Control\n', reads_edited[3], ' (', reads_edited_per[3], '%)'), paste0('No Edits in Control\n', reads_edited[4], ' (', reads_edited_per[4], '%)')) waffle(reads_edited_per, legend_pos = 'bottom', title = "Reads with indels", rows = 10, colors = c('#E69F00', '#000000', '#A9A9A9', '#F0E442')) frameshift <- c(sum(configDF$Reads_Frameshifted[!configDF$Control]), # Treatment total_reads_tmt - sum(configDF$Reads_Frameshifted[!configDF$Control]), sum(configDF$Reads_Frameshifted[configDF$Control]), # Control total_reads_ctr - sum(configDF$Reads_Frameshifted[configDF$Control])) frameshift_per <- round(frameshift*100/total_reads) frameshift_per[is.na(frameshift_per)] <- 0 names(frameshift_per) <- c( paste0('Frameshift in Treatment\n', frameshift[1], ' (', frameshift_per[1], '%)'), paste0('No Frameshift in Treatment\n', frameshift[2], ' (', frameshift_per[2], '%)'), paste0('Frameshift in Control\n', frameshift[3], ' (', frameshift_per[3], '%)'), paste0('No Frameshift in Control\n', frameshift[4], ' (', frameshift_per[4], '%)')) waffle(frameshift_per, legend_pos = 'bottom', title = "\n\nReads with frameshift", rows = 10, colors = c('#E69F00', '#000000', '#A9A9A9', '#F0E442')) ## ----fig.width=8, fig.height = height + 1, echo = F--------------------------- library(ggthemes) summaryDF_per <- summaryDF filters <- c('bad_base_quality', 'bad_average_quality', 'bad_alphabet') summaryDF_per[, filters] <- round(summaryDF_per[, filters]*100/rowSums(summaryDF_per[, filters])) summaryDF_per[, c('assigned_reads', 'unassigned_reads')] <- round(summaryDF_per[, c('assigned_reads', 'unassigned_reads')]*100/ summaryDF_per$unique_reads) summaryDF_per$bad_read_count <- summaryDF_per$read_count - summaryDF_per$filtered_read_count summaryDF_per[, c('filtered_read_count', 'bad_read_count')] <- round( summaryDF_per[, c('filtered_read_count','bad_read_count')]*100/summaryDF_per$read_count) summaryDF_per[is.na(summaryDF_per)] <- 0 summaryDF_per <- data.table::as.data.table(summaryDF_per) quality_melt <- data.table::melt(summaryDF_per, id.vars = c('Barcode'), measure.vars = c('filtered_read_count', 'bad_read_count')) quality_det_melt <- data.table::melt(summaryDF_per, id.vars = c('Barcode'), measure.vars = c('bad_base_quality', 'bad_average_quality', 'bad_alphabet')) assignment_melt <- data.table::melt(summaryDF_per, id.vars = c('Barcode'), measure.vars = c('assigned_reads', 'unassigned_reads')) ggplot(data = quality_melt, aes(x = as.factor(Barcode), y = value, fill = factor(variable, labels = c('Good Reads', 'Bad Quality Reads')))) + geom_bar(position ='stack', stat ='identity') + ylab('% of reads in barcode') + xlab('Barcode') + ggtitle('Quality filtering of reads in barcodes') + theme(legend.position = 'top', legend.direction = 'horizontal', legend.title = element_blank()) + coord_flip() + scale_fill_manual(values = c('#E69F00', '#000000')) ## ----fig.width=8, fig.height=height + 1, echo = F----------------------------- ggplot(data = quality_det_melt, aes(x = as.factor(Barcode), y = value, fill = factor(variable, labels = c('Bad Read Base Quality', 'Bad Average Read Quality', 'Bad Read Alphabet')))) + geom_bar(position='stack', stat='identity') + ylab('% of low quality reads in barcode') + xlab('Barcode') + ggtitle('\n\nDistribution of low quality reads in barcodes') + theme(legend.position = 'top', legend.direction = 'horizontal', legend.title = element_blank()) + coord_flip() + scale_color_colorblind()+ scale_fill_manual(values = c('#D55e00', '#f0e442', '#009e73')) ## ----fig.width=8, fig.height=height + 1, echo = F----------------------------- ggplot(data = assignment_melt, aes(x = as.factor(Barcode), y = value, fill = factor(variable, labels = c('Assigned Reads', 'Unassigned Reads')))) + geom_bar(position='stack', stat='identity') + ylab('% of unique reads in barcode') + xlab('Barcode') + ggtitle('\n\nAssignment of reads in barcodes') + theme(legend.position = 'top', legend.direction = 'horizontal', legend.title = element_blank()) + coord_flip() + scale_fill_manual(values = c('#E69F00', '#000000')) ## ----echo = F----------------------------------------------------------------- library(knitr) names(summaryDF) <- c("Barcodes", "Experiment Count", "Read Count", "Bad base quality", "Bad average quality", "Bad alphabet", "Good Reads", "Unique Reads", "Unassigned Reads", "Assigned Reads") kable(summaryDF)