Mercurial > repos > mingchen0919 > aurora_fastqc_site
view 05_per_base_sequence_content.Rmd @ 2:c64267b9f754 draft default tip
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author | mingchen0919 |
---|---|
date | Sun, 30 Dec 2018 12:48:14 -0500 |
parents | b7c115edd970 |
children |
line wrap: on
line source
--- 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 content ```{r 'Per base sequence content', fig.width=10} ## reads 1 pbsc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence content') pbsc_1$id = 1:length(pbsc_1$X.Base) melt_pbsc_1 = melt(pbsc_1, id=c('X.Base', 'id')) melt_pbsc_1$trim = 'before' ## reads 2 pbsc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence content') pbsc_2$id = 1:length(pbsc_2$X.Base) melt_pbsc_2 = melt(pbsc_2, id=c('X.Base', 'id')) melt_pbsc_2$trim = 'after' comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2) comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim) p = ggplot(data = comb_pbsc) + geom_line(mapping = aes(x = id, y = value, color = variable)) + facet_grid(. ~ trim) + xlim(min(comb_pbsc$id), max(comb_pbsc$id)) + ylim(0, 100) + xlab('Position in read (bp)') + ylab('') + scale_color_discrete(name = '') + theme_classic() ggplotly(p) ```