Mercurial > repos > mingchen0919 > aurora_fastqc_site
diff 07_per_base_n_content.Rmd @ 0:b7c115edd970 draft
planemo upload
author | mingchen0919 |
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date | Tue, 27 Feb 2018 10:37:12 -0500 |
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children | c64267b9f754 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/07_per_base_n_content.Rmd Tue Feb 27 10:37:12 2018 -0500 @@ -0,0 +1,38 @@ +--- +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 base N content + +```{r 'Per base N content', fig.width=10} +## reads 1 +pbNc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base N content') +pbNc_1$id = 1:length(pbNc_1$X.Base) +pbNc_1$trim = 'before' + +## reads 2 +pbNc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base N content') +pbNc_2$id = 1:length(pbNc_2$X.Base) +pbNc_2$trim = 'after' + +comb_pbNc = rbind(pbNc_1, pbNc_2) +comb_pbNc$trim = factor(levels = c('before', 'after'), comb_pbNc$trim) + +p = ggplot(data = comb_pbNc, aes(x = id, y = N.Count)) + + geom_line(color = 'red') + + scale_x_continuous(breaks = pbNc_2$id, labels = pbNc_2$X.Base) + + facet_grid(. ~ trim) + + ylim(0, 1) + + xlab('N-Count') + + ylab('') + + theme(axis.text.x = element_text(angle=45)) +ggplotly(p) +``` \ No newline at end of file