Mercurial > repos > mingchen0919 > aurora_fastqc_site
view 06_per_sequence_gc_content.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 ) ``` # Per sequence GC content ```{r 'Per sequence GC content', fig.width=10} ## reads 1 psGCc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence GC content') psGCc_1$trim = 'before' ## reads 2 psGCc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per sequence GC content') psGCc_2$trim = 'after' comb_psGCc = rbind(psGCc_1, psGCc_2) comb_psGCc$trim = factor(levels = c('before', 'after'), comb_psGCc$trim) p = ggplot(data = comb_psGCc, aes(x = X.GC.Content, y = Count)) + geom_line(color = 'red') + facet_grid(. ~ trim) + xlab('Mean Sequence Qaulity (Phred Score)') + ylab('') ggplotly(p) ```