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view 02_per_base_sequence_quality.Rmd @ 2:c64267b9f754 draft default tip
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author | mingchen0919 |
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date | Sun, 30 Dec 2018 12:48:14 -0500 |
parents | b7c115edd970 |
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--- output: html_document --- ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_knit$set(progress = FALSE) knitr::opts_chunk$set(error = TRUE, echo = FALSE) ``` ### Per base sequence quality ```{r 'per base sequence quality', fig.width=10} ## reads 1 pbsq_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence quality') pbsq_1$id = 1:length(pbsq_1$X.Base) pbsq_1$trim = 'before' ## reads 2 pbsq_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence quality') pbsq_2$id = 1:length(pbsq_2$X.Base) pbsq_2$trim = 'after' comb_pbsq = rbind(pbsq_1, pbsq_2) comb_pbsq$trim = factor(levels = c('before', 'after'), comb_pbsq$trim) p = ggplot(data = comb_pbsq) + geom_boxplot(mapping = aes(x = id, lower = Lower.Quartile, upper = Upper.Quartile, middle = Median, ymin = X10th.Percentile, ymax = X90th.Percentile, fill = "yellow"), stat = 'identity') + geom_line(mapping = aes(x = id, y = Mean, color = "red")) + scale_x_continuous(name = 'Position in read (bp)', breaks = pbsq_2$id, labels = pbsq_2$X.Base) + scale_y_continuous(limits = c(0, max(comb_pbsq$Upper.Quartile) + 5)) + scale_fill_identity() + scale_color_identity() + facet_grid(. ~ trim) + theme(axis.text.x = element_text(size = 5), panel.background = element_rect(fill = NA), panel.grid.major.y = element_line(color = 'blue', size = 0.1)) p ```