Mercurial > repos > mingchen0919 > aurora_fastqc_site
view 09_sequence_duplication_levels.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 ) ``` # Sequence Duplication Levels ```{r 'Sequence Duplication Levels', fig.width=10} ## reads 1 sdl_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#') names(sdl_1) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total') sdl_1$id = 1:length(sdl_1$Duplication_Level) melt_sdl_1 = melt(sdl_1, id=c('Duplication_Level', 'id')) melt_sdl_1$trim = 'before' ## reads 2 sdl_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#') names(sdl_2) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total') sdl_2$id = 1:length(sdl_2$Duplication_Level) melt_sdl_2 = melt(sdl_2, id=c('Duplication_Level', 'id')) melt_sdl_2$trim = 'after' comb_sdl = rbind(melt_sdl_1, melt_sdl_2) comb_sdl$trim = factor(levels = c('before', 'after'), comb_sdl$trim) p = ggplot(data = comb_sdl, aes(x = id, y = value, color = variable)) + geom_line() + scale_x_continuous(breaks = sdl_2$id, labels = sdl_2$Duplication_Level) + facet_grid(. ~ trim) + xlab('Sequence Duplication Level') + ylab('') + theme(axis.text.x = element_text(angle=45)) ggplotly(p) ```