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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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3
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14 ### Per base sequence quality
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1
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15
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16 ```{r 'per base sequence quality', fig.width=10}
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17 ## reads 1
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18 pbsq_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence quality')
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19 pbsq_1$id = 1:length(pbsq_1$X.Base)
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20 pbsq_1$trim = 'before'
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21
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22 ## reads 2
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23 pbsq_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence quality')
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24 pbsq_2$id = 1:length(pbsq_2$X.Base)
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25 pbsq_2$trim = 'after'
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26
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27 comb_pbsq = rbind(pbsq_1, pbsq_2)
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28 comb_pbsq$trim = factor(levels = c('before', 'after'), comb_pbsq$trim)
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29
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30 p = ggplot(data = comb_pbsq) +
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31 geom_boxplot(mapping = aes(x = id,
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32 lower = Lower.Quartile,
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33 upper = Upper.Quartile,
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34 middle = Median,
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35 ymin = X10th.Percentile,
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36 ymax = X90th.Percentile,
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37 fill = "yellow"),
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38 stat = 'identity') +
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39 geom_line(mapping = aes(x = id, y = Mean, color = "red")) +
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40 scale_x_continuous(name = 'Position in read (bp)', breaks = pbsq_2$id, labels = pbsq_2$X.Base) +
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41 scale_y_continuous(limits = c(0, max(comb_pbsq$Upper.Quartile) + 5)) +
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42 scale_fill_identity() +
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43 scale_color_identity() +
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44 facet_grid(. ~ trim) +
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45 theme(axis.text.x = element_text(size = 5),
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46 panel.background = element_rect(fill = NA),
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47 panel.grid.major.y = element_line(color = 'blue', size = 0.1))
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48 p
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3
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49 ```
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50
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