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11
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1 ---
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2 title: 'Per Tile 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$set(
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13 echo = ECHO,
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14 error = TRUE
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15 )
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16 ```
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17
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18 ### Per tile sequence quality
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19
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20 ```{r 'per tile sequence quality', fig.width=10}
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21 ## check if 'per tile sequence quality' module exits or not
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22 check_ptsq = grep('Per tile sequence quality', readLines('REPORT_DIR/reads_1_fastqc_data.txt'))
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23 if (length(check_ptsq) > 0) {
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24 ## reads 1
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25 ptsq_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per tile sequence quality')
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26 ptsq_1$trim = 'before'
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27
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28 ## reads 2
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29 ptsq_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per tile sequence quality')
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30 ptsq_2$trim = 'after'
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31
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32 comb_ptsq = rbind(ptsq_1, ptsq_2)
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33 comb_ptsq$trim = factor(levels = c('before', 'after'), comb_ptsq$trim)
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34 comb_ptsq$Base = factor(levels = unique(comb_ptsq$Base), comb_ptsq$Base)
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35
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36 # convert integers to charaters
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37 comb_ptsq$Tile = as.character(comb_ptsq$X.Tile)
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38
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39 p = ggplot(data = comb_ptsq, aes(x = Base, y = Tile, fill = Mean)) +
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40 geom_raster() +
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41 facet_grid(. ~ trim) +
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42 xlab('Position in read (bp)') +
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43 ylab('') +
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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 } else {
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47 print('No "per tile sequence quality" data')
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48 } |
