Mercurial > repos > mingchen0919 > aurora_fastqc_site
view 02_per_base_sequence_quality.Rmd @ 1:92e3de11b9f8 draft
remove fastqc_report.Rmd
author | mingchen0919 |
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date | Tue, 27 Feb 2018 10:40:20 -0500 |
parents | b7c115edd970 |
children | c64267b9f754 |
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--- output: html_document --- ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_chunk$set( echo = as.logical(opt$X_e), error = TRUE, eval = TRUE ) ``` ```{r 'function definition', echo=FALSE} # Define a function to extract outputs for each module from fastqc output extract_data_module = function(fastqc_data, module_name, header = TRUE, comment.char = "") { f = readLines(fastqc_data) start_line = grep(module_name, f) end_module_lines = grep('END_MODULE', f) end_line = end_module_lines[which(end_module_lines > start_line)[1]] module_data = f[(start_line+1):(end_line-1)] writeLines(module_data, '/tmp/temp.txt') read.csv('/tmp/temp.txt', sep = '\t', header = header, comment.char = comment.char) } ``` # 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(breaks = pbsq_2$id, labels = pbsq_2$X.Base) + scale_fill_identity() + scale_color_identity() + ylim(0, max(comb_pbsq$Upper.Quartile) + 5) + xlab('Position in read (bp)') + facet_grid(. ~ trim) + theme(axis.text.x = element_text(angle=45)) p ```