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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 # Per base sequence content
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15
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16 ```{r 'Per base sequence content', fig.width=10}
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17 ## reads 1
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18 pbsc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence content')
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19 pbsc_1$id = 1:length(pbsc_1$X.Base)
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20
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21 melt_pbsc_1 = melt(pbsc_1, id=c('X.Base', 'id'))
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22 melt_pbsc_1$trim = 'before'
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23
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24
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25 ## reads 2
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26 pbsc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence content')
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27 pbsc_2$id = 1:length(pbsc_2$X.Base)
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28
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29 melt_pbsc_2 = melt(pbsc_2, id=c('X.Base', 'id'))
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30 melt_pbsc_2$trim = 'after'
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31
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32 comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2)
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33 comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim)
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34
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35 p = ggplot(data = comb_pbsc, aes(x = id, y = value, color = variable)) +
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36 geom_line() +
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37 facet_grid(. ~ trim) +
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38 xlim(min(comb_pbsc$id), max(comb_pbsc$id)) +
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39 ylim(0, 100) +
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40 xlab('Position in read (bp)') +
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41 ylab('')
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42 ggplotly(p)
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43 ``` |
