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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 sequence quality score
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15
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16 ```{r 'Per sequence quality score', fig.width=10}
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17 ## reads 1
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18 psqs_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence quality scores')
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19 psqs_1$trim = 'before'
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20
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21 ## reads 2
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22 psqs_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per sequence quality scores')
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23 psqs_2$trim = 'after'
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24
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25 comb_psqs = rbind(psqs_1, psqs_2)
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26 comb_psqs$trim = factor(levels = c('before', 'after'), comb_psqs$trim)
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27
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28 p = ggplot(data = comb_psqs, aes(x = X.Quality, y = Count)) +
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29 geom_line(color = 'red') +
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30 facet_grid(. ~ trim) +
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31 xlim(min(comb_psqs$X.Quality), max(comb_psqs$X.Quality)) +
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32 xlab('Mean Sequence Qaulity (Phred Score)') +
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33 ylab('')
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34 ggplotly(p)
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35 ```
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