Mercurial > repos > mingchen0919 > aurora_fastqc_site

annotate 03_per_tile_sequence_quality.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 tile sequence quality
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12 ```{r 'per tile sequence quality', fig.width=10}
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13 ## check if 'per tile sequence quality' module exits or not
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14 check_ptsq = grep('Per tile sequence quality', readLines(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt')))
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15 if (length(check_ptsq) > 0) {
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16 ## reads 1
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17 ptsq_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per tile sequence quality')
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18 ptsq_1$trim = 'before'
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19
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20 ## reads 2
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21 ptsq_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per tile sequence quality')
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22 ptsq_2$trim = 'after'
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23
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24 comb_ptsq = rbind(ptsq_1, ptsq_2)
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25 comb_ptsq$trim = factor(levels = c('before', 'after'), comb_ptsq$trim)
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26 comb_ptsq$Base = factor(levels = unique(comb_ptsq$Base), comb_ptsq$Base)
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27
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28 # convert integers to charaters
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29 # comb_ptsq$Tile = as.character(comb_ptsq$X.Tile)
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30
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31 p = ggplot(data = comb_ptsq) +
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32 geom_raster(mapping = aes(x = Base, y = X.Tile, fill = Mean)) +
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33 facet_grid(. ~ trim) +
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34 scale_x_discrete(name = "Position in read (bp)") +
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35 scale_y_continuous(name = "") +
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36 scale_fill_gradient(low = "blue", high = "red") +
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37 theme(axis.text.x = element_text(size = 5, angle = 90),
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38 axis.text.y = element_text(size = 5),
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39 panel.background = element_rect(fill = NA))
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40 ggplotly(p)
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41 } else {
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42 print('No "per tile sequence quality" data')
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43 }
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44 ```