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11
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1 ---
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2 title: 'Per base sequence quality'
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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$set(
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13 echo = ECHO,
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14 error = TRUE
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15 )
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16 ```
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17
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18 ### Per base sequence quality
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19
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20 ```{r 'per base sequence quality', fig.width=10}
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21 ## reads 1
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22 pbsq_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per base sequence quality')
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23 pbsq_1$id = 1:length(pbsq_1$X.Base)
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24
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25 melt_pbsq_1 = filter(melt(pbsq_1, id=c('X.Base', 'id')), variable == 'Mean')
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26 melt_pbsq_1$trim = 'before'
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27
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28
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29 ## reads 2
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30 pbsq_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per base sequence quality')
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31 pbsq_2$id = 1:length(pbsq_2$X.Base)
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32
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33 melt_pbsq_2 = filter(melt(pbsq_2, id=c('X.Base', 'id')), variable == 'Mean')
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34 melt_pbsq_2$trim = 'after'
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35
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36 comb_pbsq = rbind(melt_pbsq_1, melt_pbsq_2)
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37 comb_pbsq$trim = factor(levels = c('before', 'after'), comb_pbsq$trim)
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38
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39 p = ggplot(data = comb_pbsq) +
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40 geom_line(mapping = aes(x = id, y = value, group = variable, color = variable)) +
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41 scale_x_continuous(breaks = pbsq_2$id, labels = pbsq_2$X.Base) +
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42 facet_grid(. ~ trim) +
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43 ylim(0, max(comb_pbsq$value) + 5) +
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44 theme(axis.text.x = element_text(angle=45))
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45 ggplotly(p)
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46
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47 ``` |
