Mercurial > repos > mingchen0919 > aurora_fastqc_site

annotate 08_sequence_length_distribution.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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4
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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 ### Sequence Length Distribution
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12 ```{r 'Sequence Length Distribution', fig.width=10}
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13 ## reads 1
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14 sld_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Length Distribution')
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15 sld_1$id = 1:length(sld_1$X.Length)
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16 sld_1$trim = 'before'
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17
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18 ## reads 2
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19 sld_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Length Distribution')
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20 sld_2$id = 1:length(sld_2$X.Length)
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21 sld_2$trim = 'after'
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22
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23 comb_sld = rbind(sld_1, sld_2)
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24 comb_sld$trim = factor(levels = c('before', 'after'), comb_sld$trim)
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25
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26 p = ggplot(data = comb_sld, aes(x = id, y = Count)) +
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27 geom_line(color = 'red') +
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28 scale_x_continuous(breaks = sld_2$id, labels = sld_2$X.Length) +
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29 facet_grid(. ~ trim) +
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30 xlab('Sequence Length (bp)') +
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31 ylab('') +
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32 theme(axis.text.x = element_text(size = 5),
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33 panel.background = element_rect(fill = NA),
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34 axis.line = element_line(),
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35 plot.margin = margin(2,2,2,10) )
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36 ggplotly(p)
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37 ```