Mercurial > repos > mingchen0919 > aurora_fastqc_site
annotate 02_per_base_sequence_quality.Rmd @ 8:94762f1cb779 draft
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
| author | mingchen0919 |
|---|---|
| date | Mon, 30 Apr 2018 16:15:39 -0400 |
| parents | b9c9d1dacda6 |
| children |
| rev | line source |
|---|---|
| 1 | 1 --- |
| 2 output: html_document | |
| 3 --- | |
| 4 | |
| 5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
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94762f1cb779
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
mingchen0919
parents:
3
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changeset
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6 knitr::opts_knit$set(progress = FALSE) |
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94762f1cb779
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
mingchen0919
parents:
3
diff
changeset
|
7 knitr::opts_chunk$set(error = TRUE, echo = FALSE) |
| 1 | 8 ``` |
| 9 | |
| 3 | 10 ### Per base sequence quality |
| 1 | 11 |
| 12 ```{r 'per base sequence quality', fig.width=10} | |
| 13 ## reads 1 | |
| 14 pbsq_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence quality') | |
| 15 pbsq_1$id = 1:length(pbsq_1$X.Base) | |
| 16 pbsq_1$trim = 'before' | |
| 17 | |
| 18 ## reads 2 | |
| 19 pbsq_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence quality') | |
| 20 pbsq_2$id = 1:length(pbsq_2$X.Base) | |
| 21 pbsq_2$trim = 'after' | |
| 22 | |
| 23 comb_pbsq = rbind(pbsq_1, pbsq_2) | |
| 24 comb_pbsq$trim = factor(levels = c('before', 'after'), comb_pbsq$trim) | |
| 25 | |
| 26 p = ggplot(data = comb_pbsq) + | |
| 27 geom_boxplot(mapping = aes(x = id, | |
| 28 lower = Lower.Quartile, | |
| 29 upper = Upper.Quartile, | |
| 30 middle = Median, | |
| 31 ymin = X10th.Percentile, | |
| 32 ymax = X90th.Percentile, | |
| 33 fill = "yellow"), | |
| 34 stat = 'identity') + | |
| 35 geom_line(mapping = aes(x = id, y = Mean, color = "red")) + | |
| 3 | 36 scale_x_continuous(name = 'Position in read (bp)', breaks = pbsq_2$id, labels = pbsq_2$X.Base) + |
| 37 scale_y_continuous(limits = c(0, max(comb_pbsq$Upper.Quartile) + 5)) + | |
| 1 | 38 scale_fill_identity() + |
| 39 scale_color_identity() + | |
| 40 facet_grid(. ~ trim) + | |
| 3 | 41 theme(axis.text.x = element_text(size = 5), |
| 42 panel.background = element_rect(fill = NA), | |
| 43 panel.grid.major.y = element_line(color = 'blue', size = 0.1)) | |
| 1 | 44 p |
| 3 | 45 ``` |
| 1 | 46 |