Mercurial > repos > mingchen0919 > aurora_fastqc_site
view 04_per_sequence_quality_score.Rmd @ 0:b7c115edd970 draft
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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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--- 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 quality score ```{r 'Per sequence quality score', fig.width=10} ## reads 1 psqs_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence quality scores') psqs_1$trim = 'before' ## reads 2 psqs_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per sequence quality scores') psqs_2$trim = 'after' comb_psqs = rbind(psqs_1, psqs_2) comb_psqs$trim = factor(levels = c('before', 'after'), comb_psqs$trim) p = ggplot(data = comb_psqs, aes(x = X.Quality, y = Count)) + geom_line(color = 'red') + facet_grid(. ~ trim) + xlim(min(comb_psqs$X.Quality), max(comb_psqs$X.Quality)) + xlab('Mean Sequence Qaulity (Phred Score)') + ylab('') ggplotly(p) ```