comparison fastqc_report.Rmd @ 19:8c79e5b7cfc0 draft default tip

add boxplot for per base sequence quality

18:8635a4cee6dd

  geom_line(mapping = aes(x = id, y = Mean, color = "red")) +
  scale_x_continuous(breaks = pbsq_2$id, labels = pbsq_2$X.Base) +
  scale_fill_identity() +
  scale_color_identity() + 
  ylim(0, max(comb_pbsq$Upper.Quartile) + 5) +
  facet_grid(. ~ trim) +
  theme(axis.text.x = element_text(angle=45))
p

```

```{r 'session info'}
sessionInfo()
```

19:8c79e5b7cfc0

  geom_line(mapping = aes(x = id, y = Mean, color = "red")) +
  scale_x_continuous(breaks = pbsq_2$id, labels = pbsq_2$X.Base) +
  scale_fill_identity() +
  scale_color_identity() + 
  ylim(0, max(comb_pbsq$Upper.Quartile) + 5) +
  xlab('Position in read (bp)') +
  facet_grid(. ~ trim) +
  theme(axis.text.x = element_text(angle=45))
p

```

```{r 'session info'}
sessionInfo()
```

# References

* Bioinformatics, Babraham (2014). FastQC.

* Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob (2016). rmarkdown: Dynamic Documents for R, 2016. In R package version 0.9, 6.

* Xie, Yihui (2015). Dynamic Documents with R and knitr, CRC Press, Vol.29.

* Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. [Link]

* Wickham, H. (2016). ggplot2: elegant graphics for data analysis. Springer. Chicago