Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site
view 02_per_base_sequence_quality.Rmd @ 14:a6bf4dfca096 draft
remove unnecessary dependencies
author | mingchen0919 |
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date | Thu, 09 Nov 2017 09:32:42 -0500 |
parents | 68ea2ebbf866 |
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--- title: 'Per base sequence quality' output: html_document: number_sections: true toc: true theme: cosmo highlight: tango --- ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_chunk$set( echo = ECHO, error = TRUE ) ``` ### Per base sequence quality ```{r 'per base sequence quality', fig.width=10} ## reads 1 pbsq_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per base sequence quality') pbsq_1$id = 1:length(pbsq_1$X.Base) pbsq_1$trim = 'before' ## reads 2 pbsq_2 = extract_data_module('REPORT_DIR/reads_2_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 ```