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view 04_per_sequence_quality_score.Rmd @ 2:c64267b9f754 draft default tip
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author | mingchen0919 |
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date | Sun, 30 Dec 2018 12:48:14 -0500 |
parents | b7c115edd970 |
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--- 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 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) + geom_line(mapping = aes(x = X.Quality, y = Count), color = 'red') + facet_grid(. ~ trim) + scale_x_continuous(name = 'Mean Sequence Qaulity (Phred Score)', limits = c(min(comb_psqs$X.Quality), max(comb_psqs$X.Quality))) + scale_y_continuous(name = '') + theme(panel.background = element_rect(fill = NA), axis.line = element_line(), panel.grid.major.y = element_line(color = 'blue', size = 0.1)) p ```