Mercurial > repos > mingchen0919 > aurora_fastqc_site

annotate 10_adapter_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
children
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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 ### Adapter Content
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12 ```{r 'Adapter Content', fig.width=10}
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13 ## reads 1
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14 ac_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Adapter Content')
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15 ac_1$id = 1:length(ac_1$X.Position)
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16
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17 melt_ac_1 = melt(ac_1, id=c('X.Position', 'id'))
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18 melt_ac_1$trim = 'before'
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19
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20 ## reads 2
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21 ac_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Adapter Content')
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22 ac_2$id = 1:length(ac_2$X.Position)
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23
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24 melt_ac_2 = melt(ac_2, id=c('X.Position', 'id'))
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25 melt_ac_2$trim = 'after'
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26
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27 comb_ac = rbind(melt_ac_1, melt_ac_2)
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28 comb_ac$trim = factor(levels = c('before', 'after'), comb_ac$trim)
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29
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30 p = ggplot(data = comb_ac, aes(x = id, y = value, color = variable)) +
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31 geom_line() +
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32 facet_grid(. ~ trim) +
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33 xlim(min(comb_ac$id), max(comb_ac$id)) +
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34 ylim(0, 1) +
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35 xlab('Position in read (bp)') +
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36 ylab('') +
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37 scale_color_discrete(name = '') +
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38 theme(axis.text.x = element_text(size = 5),
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39 panel.background = element_rect(fill = NA),
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40 axis.line = element_line())
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41 ggplotly(p)
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42 ```