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11
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1 ---
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2 title: 'Per base sequence 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$set(
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13 echo = ECHO,
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14 error = TRUE
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15 )
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16 ```
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17
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18 ### Per base sequence content
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19
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20 ```{r 'Per base sequence content', fig.width=10}
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21 ## reads 1
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22 pbsc_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per base sequence content')
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23 pbsc_1$id = 1:length(pbsc_1$X.Base)
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24
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25 melt_pbsc_1 = melt(pbsc_1, id=c('X.Base', 'id'))
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26 melt_pbsc_1$trim = 'before'
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27
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28
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29 ## reads 2
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30 pbsc_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per base sequence content')
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31 pbsc_2$id = 1:length(pbsc_2$X.Base)
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32
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33 melt_pbsc_2 = melt(pbsc_2, id=c('X.Base', 'id'))
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34 melt_pbsc_2$trim = 'after'
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35
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36 comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2)
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37 comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim)
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38
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39 p = ggplot(data = comb_pbsc, aes(x = id, y = value, color = variable)) +
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40 geom_line() +
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41 facet_grid(. ~ trim) +
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42 xlim(min(comb_pbsc$id), max(comb_pbsc$id)) +
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43 ylim(0, 100) +
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44 xlab('Position in read (bp)') +
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45 ylab('')
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46 ggplotly(p)
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47 ``` |
