Mercurial > repos > mingchen0919 > aurora_fastqc_site

annotate 09_sequence_duplication_levels.Rmd @ 2:c64267b9f754 draft default tip

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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 12:48:14 -0500
parents b7c115edd970
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1 ---
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2 output: html_document
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3 ---
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5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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6 knitr::opts_knit$set(progress = FALSE)
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7 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
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8 ```
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9
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11 ### Sequence Duplication Levels
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13 ```{r 'Sequence Duplication Levels', fig.width=10}
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14 ## reads 1
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15 sdl_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#')
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16 names(sdl_1) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total')
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17 sdl_1$id = 1:length(sdl_1$Duplication_Level)
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19 melt_sdl_1 = melt(sdl_1, id=c('Duplication_Level', 'id'))
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20 melt_sdl_1$trim = 'before'
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23 ## reads 2
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24 sdl_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#')
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25 names(sdl_2) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total')
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26 sdl_2$id = 1:length(sdl_2$Duplication_Level)
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27
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28 melt_sdl_2 = melt(sdl_2, id=c('Duplication_Level', 'id'))
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29 melt_sdl_2$trim = 'after'
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30
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31 comb_sdl = rbind(melt_sdl_1, melt_sdl_2)
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32 comb_sdl$trim = factor(levels = c('before', 'after'), comb_sdl$trim)
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33
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34 p = ggplot(data = comb_sdl) +
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35 geom_line(mapping = aes(x = id, y = value, color = variable)) +
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36 scale_x_continuous(breaks = sdl_2$id, labels = sdl_2$Duplication_Level) +
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37 facet_grid(. ~ trim) +
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38 xlab('Sequence Duplication Level') +
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39 ylab('') +
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40 scale_color_discrete(name = '') +
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41 theme(axis.text.x = element_text(size = 5),
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42 panel.background = element_rect(fill = NA),
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43 axis.line = element_line())
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44 p
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45 ```