Mercurial > repos > mingchen0919 > aurora_fastqc_site

annotate 06_per_sequence_gc_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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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 sequence GC content
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12 ```{r 'Per sequence GC content', fig.width=10}
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13 ## reads 1
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14 psGCc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence GC content')
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15 psGCc_1$trim = 'before'
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16
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17 ## reads 2
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18 psGCc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per sequence GC content')
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19 psGCc_2$trim = 'after'
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21 comb_psGCc = rbind(psGCc_1, psGCc_2)
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22 comb_psGCc$trim = factor(levels = c('before', 'after'), comb_psGCc$trim)
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23
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24 p = ggplot(data = comb_psGCc, aes(x = X.GC.Content, y = Count)) +
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25 geom_line(color = 'red') +
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26 facet_grid(. ~ trim) +
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27 xlab('Mean Sequence Qaulity (Phred Score)') +
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28 ylab('') +
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29 scale_color_discrete(name = '') +
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30 theme_classic()
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31 ggplotly(p)
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32 ```