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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 # Adapter Content
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14
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15 ```{r 'Adapter Content', fig.width=10}
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16 ## reads 1
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17 ac_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Adapter Content')
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18 ac_1$id = 1:length(ac_1$X.Position)
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19
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20 melt_ac_1 = melt(ac_1, id=c('X.Position', 'id'))
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21 melt_ac_1$trim = 'before'
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22
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23 ## reads 2
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24 ac_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Adapter Content')
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25 ac_2$id = 1:length(ac_2$X.Position)
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26
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27 melt_ac_2 = melt(ac_2, id=c('X.Position', 'id'))
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28 melt_ac_2$trim = 'after'
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29
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30 comb_ac = rbind(melt_ac_1, melt_ac_2)
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31 comb_ac$trim = factor(levels = c('before', 'after'), comb_ac$trim)
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32
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33 p = ggplot(data = comb_ac, aes(x = id, y = value, color = variable)) +
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34 geom_line() +
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35 facet_grid(. ~ trim) +
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36 xlim(min(comb_ac$id), max(comb_ac$id)) +
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37 ylim(0, 1) +
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38 xlab('Position in read (bp)') +
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39 ylab('')
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40 ggplotly(p)
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41 ``` |
