params <- list(alignments = "/tmp/Rtmpz7DMgw/Rinst1c193125742589/amplican/extdata/results/alignments/events_filtered_shifted_normalized.csv", config_summary = "/tmp/Rtmpz7DMgw/Rinst1c193125742589/amplican/extdata/results/config_summary.csv", cut_buffer = 5L, xlab_spacing = 4L) ## ----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 <- plot_height(length(unique(config$ID))) ## ----plot_total_reads, echo=FALSE, fig.height=height, fig.width=14, message=F, warning=FALSE---- ggplot(data = config, aes(x = as.factor(ID), y = log10(Reads + 1), order = ID)) + geom_bar(stat='identity') + ylab('Number of reads + 1, log10 scaled') + xlab('ID') + theme(legend.position = 'none', axis.text = element_text(size = 12), axis.title = element_text(size = 14, face = 'bold')) + coord_flip() + geom_text(aes(x = as.factor(ID), y = log10(Reads + 1), label = Reads), hjust = -1) ## ----plot_F_per, echo=FALSE, fig.height=height, fig.width=14, message=F, warning=FALSE---- config$PRIMER_DIMER <- config$PRIMER_DIMER * 100/config$Reads config$PRIMER_DIMER[is.nan(config$PRIMER_DIMER)] <- 0 config$Low_Score <- config$Low_Score * 100/config$Reads config$Low_Score[is.nan(config$Low_Score)] <- 0 config_melt <- data.table::melt(data.table::as.data.table(config), id.vars = "ID", measure.vars = c("PRIMER_DIMER", "Low_Score")) ggplot(data = config_melt, aes(x = as.factor(ID), y = value, fill = variable, order = ID)) + geom_bar(stat='identity') + ylab('Percentage of filtered reads') + xlab('ID') + theme(legend.position = 'top', axis.text = element_text(size = 12), axis.title = element_text(size = 14, face = 'bold')) + coord_flip() + labs(fill = "") ## ----plot mut percentage, echo=FALSE, fig.height=height, fig.width=14, message=F, warning=FALSE---- config$edit_percentage <- config$Reads_Edited * 100/config$Reads_Filtered config$edit_percentage[is.nan(config$edit_percentage)] <- 0 ggplot(data = config, aes(x = as.factor(ID), y = edit_percentage, order = ID)) + geom_bar(stat='identity') + ylab('Percentage of reads (not filtered) that have edits') + xlab('ID') + theme(legend.position = 'none', axis.text = element_text(size = 12), axis.title = element_text(size = 14, face = 'bold')) + coord_flip() + geom_text(aes(x = as.factor(ID), y = edit_percentage, label = Reads_Edited), hjust = -1) ## ----plot_frameshift_per, echo=FALSE, fig.height=height, fig.width=14, message=F, warning=FALSE---- config$frameshift_percentage <- config$Reads_Frameshifted * 100/config$Reads_Filtered config$frameshift_percentage[is.nan(config$frameshift_percentage)] <- 0 ggplot(data = config, aes(x = as.factor(ID), y = frameshift_percentage, order = ID)) + geom_bar(stat='identity') + ylab('Percentage of reads (not filtered) that have frameshift') + xlab('ID') + theme(legend.position = 'none', axis.text = element_text(size = 12), axis.title = element_text(size = 14, face = 'bold')) + coord_flip() + geom_text(aes(x = as.factor(ID), y = frameshift_percentage, label = Reads_Frameshifted), hjust = -1) ## ----plot read domination, echo=FALSE, fig.height=height + 1, fig.width=14, message=F, warning=FALSE---- plot_heterogeneity(alignments, config) ## ----del-ID_1, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_deletions(alignments, config, "ID_1", params$cut_buffer, params$xlab_spacing) ## ----ins-ID_1, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_insertions(alignments, config, "ID_1", params$cut_buffer, params$xlab_spacing) ## ----mis-ID_1, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_mismatches(alignments, config, "ID_1", params$cut_buffer, params$xlab_spacing) ## ----var-ID_1, echo = F, message=F, results = "asis", message=F, warning=F---- p <- amplican::plot_variants(alignments_cons, config, "ID_1", params$cut_buffer) ## ----del-ID_2, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_deletions(alignments, config, "ID_2", params$cut_buffer, params$xlab_spacing) ## ----ins-ID_2, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_insertions(alignments, config, "ID_2", params$cut_buffer, params$xlab_spacing) ## ----mis-ID_2, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_mismatches(alignments, config, "ID_2", params$cut_buffer, params$xlab_spacing) ## ----var-ID_2, echo = F, message=F, results = "asis", message=F, warning=F---- p <- amplican::plot_variants(alignments_cons, config, "ID_2", params$cut_buffer) ## ----del-ID_3, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_deletions(alignments, config, "ID_3", params$cut_buffer, params$xlab_spacing) ## ----ins-ID_3, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_insertions(alignments, config, "ID_3", params$cut_buffer, params$xlab_spacing) ## ----mis-ID_3, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_mismatches(alignments, config, "ID_3", params$cut_buffer, params$xlab_spacing) ## ----var-ID_3, echo = F, message=F, results = "asis", message=F, warning=F---- p <- amplican::plot_variants(alignments_cons, config, "ID_3", params$cut_buffer) ## ----del-ID_4, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_deletions(alignments, config, "ID_4", params$cut_buffer, params$xlab_spacing) ## ----ins-ID_4, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_insertions(alignments, config, "ID_4", params$cut_buffer, params$xlab_spacing) ## ----mis-ID_4, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_mismatches(alignments, config, "ID_4", params$cut_buffer, params$xlab_spacing) ## ----var-ID_4, echo = F, message=F, results = "asis", message=F, warning=F---- p <- amplican::plot_variants(alignments_cons, config, "ID_4", params$cut_buffer) ## ----del-ID_5, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_deletions(alignments, config, "ID_5", params$cut_buffer, params$xlab_spacing) ## ----ins-ID_5, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_insertions(alignments, config, "ID_5", params$cut_buffer, params$xlab_spacing) ## ----mis-ID_5, echo = F, results = "asis", fig.width=25, message=F, warning=F---- p <- amplican::plot_mismatches(alignments, config, "ID_5", params$cut_buffer, params$xlab_spacing) ## ----var-ID_5, echo = F, message=F, results = "asis", message=F, warning=F---- p <- amplican::plot_variants(alignments_cons, config, "ID_5", params$cut_buffer) ## ----plot_alignments, results='asis', echo=F, message=F, warning=F------------ alignments_cons <- alignments[alignments$consensus & alignments$overlaps, ] src = sapply(config$ID, function(i) { knitr::knit_expand(text = c( "## {{i}} \n", "### Deletions \n", paste('```{r del-{{i}}, echo = F, results = "asis", ', 'fig.width=25, message=F, warning=F}', collapse = ''), paste('p <- amplican::plot_deletions(alignments, config, "{{i}}",', ' params$cut_buffer, params$xlab_spacing)', collapse = ''), '```\n', "### Insertions \n", paste('```{r ins-{{i}}, echo = F, results = "asis", ', 'fig.width=25, message=F, warning=F}', collapse = ''), paste('p <- amplican::plot_insertions(alignments, config, "{{i}}",', ' params$cut_buffer, params$xlab_spacing)', collapse = ''), '```\n', "### Mismatches \n", paste('```{r mis-{{i}}, echo = F, results = "asis", ', 'fig.width=25, message=F, warning=F}', collapse = ''), paste('p <- amplican::plot_mismatches(alignments, config, "{{i}}",', ' params$cut_buffer, params$xlab_spacing)', collapse = ''), '```\n', "### Variants \n", paste('```{r var-{{i}}, echo = F, message=F, results = "asis", ', 'message=F, warning=F}', collapse = ''), paste('p <- amplican::plot_variants(alignments_cons, config, "{{i}}", ', ' params$cut_buffer)', collapse = ''), '```\n')) }) # knit the source res = knitr::knit_child(text = src, quiet = TRUE) cat(res, sep = '\n')