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1 ---
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2 output: html_document
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3 ---
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4
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5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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6 knitr::opts_chunk$set(
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7 echo = as.logical(opt$X_e),
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8 error = TRUE,
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9 eval = TRUE
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10 )
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11 ```
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12
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13
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14 # Sequence Duplication Levels
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15
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16 ```{r 'Sequence Duplication Levels', fig.width=10}
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17 ## reads 1
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18 sdl_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#')
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19 names(sdl_1) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total')
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20 sdl_1$id = 1:length(sdl_1$Duplication_Level)
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21
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22 melt_sdl_1 = melt(sdl_1, id=c('Duplication_Level', 'id'))
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23 melt_sdl_1$trim = 'before'
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24
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25
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26 ## reads 2
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27 sdl_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#')
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28 names(sdl_2) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total')
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29 sdl_2$id = 1:length(sdl_2$Duplication_Level)
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30
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31 melt_sdl_2 = melt(sdl_2, id=c('Duplication_Level', 'id'))
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32 melt_sdl_2$trim = 'after'
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33
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34 comb_sdl = rbind(melt_sdl_1, melt_sdl_2)
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35 comb_sdl$trim = factor(levels = c('before', 'after'), comb_sdl$trim)
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36
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37 p = ggplot(data = comb_sdl, aes(x = id, y = value, color = variable)) +
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38 geom_line() +
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39 scale_x_continuous(breaks = sdl_2$id, labels = sdl_2$Duplication_Level) +
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40 facet_grid(. ~ trim) +
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41 xlab('Sequence Duplication Level') +
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42 ylab('') +
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43 theme(axis.text.x = element_text(angle=45))
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44 ggplotly(p)
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45 ``` |
