Mercurial > repos > mingchen0919 > aurora_fastqc_site

annotate 05_per_base_sequence_content.Rmd @ 2:c64267b9f754 draft default tip

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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 12:48:14 -0500
parents b7c115edd970
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1 ---
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2 output: html_document
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3 ---
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5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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6 knitr::opts_knit$set(progress = FALSE)
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7 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
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8 ```
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9
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10 ### Per base sequence content
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12 ```{r 'Per base sequence content', fig.width=10}
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13 ## reads 1
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14 pbsc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence content')
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15 pbsc_1$id = 1:length(pbsc_1$X.Base)
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16
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17 melt_pbsc_1 = melt(pbsc_1, id=c('X.Base', 'id'))
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18 melt_pbsc_1$trim = 'before'
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21 ## reads 2
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22 pbsc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence content')
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23 pbsc_2$id = 1:length(pbsc_2$X.Base)
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24
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25 melt_pbsc_2 = melt(pbsc_2, id=c('X.Base', 'id'))
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26 melt_pbsc_2$trim = 'after'
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27
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28 comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2)
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29 comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim)
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30
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31 p = ggplot(data = comb_pbsc) +
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32 geom_line(mapping = aes(x = id, y = value, color = variable)) +
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33 facet_grid(. ~ trim) +
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34 xlim(min(comb_pbsc$id), max(comb_pbsc$id)) +
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35 ylim(0, 100) +
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36 xlab('Position in read (bp)') +
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37 ylab('') +
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38 scale_color_discrete(name = '') +
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39 theme_classic()
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40 ggplotly(p)
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41 ```