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11
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1 ---
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2 title: 'Adapter Content'
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3 output:
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4 html_document:
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5 number_sections: true
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6 toc: true
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7 theme: cosmo
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8 highlight: tango
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9 ---
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10
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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12 knitr::opts_chunk$set(
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13 echo = ECHO,
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14 error = TRUE
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15 )
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16 ```
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17
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18 ### Adapter Content
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19
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20 ```{r 'Adapter Content', fig.width=10}
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21 ## reads 1
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22 ac_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Adapter Content')
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23 ac_1$id = 1:length(ac_1$X.Position)
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24
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25 melt_ac_1 = melt(ac_1, id=c('X.Position', 'id'))
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26 melt_ac_1$trim = 'before'
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27
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28 ## reads 2
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29 ac_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Adapter Content')
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30 ac_2$id = 1:length(ac_2$X.Position)
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31
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32 melt_ac_2 = melt(ac_2, id=c('X.Position', 'id'))
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33 melt_ac_2$trim = 'after'
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34
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35 comb_ac = rbind(melt_ac_1, melt_ac_2)
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36 comb_ac$trim = factor(levels = c('before', 'after'), comb_ac$trim)
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37
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38 p = ggplot(data = comb_ac, aes(x = id, y = value, color = variable)) +
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39 geom_line() +
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40 facet_grid(. ~ trim) +
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41 xlim(min(comb_ac$id), max(comb_ac$id)) +
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42 ylim(0, 1) +
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43 xlab('Position in read (bp)') +
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44 ylab('')
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45 ggplotly(p)
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46 ``` |
