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

add boxplot for per base sequence quality

--- a/fastqc_report.Rmd	Thu Nov 09 09:22:09 2017 -0500
+++ b/fastqc_report.Rmd	Thu Nov 09 09:49:46 2017 -0500
@@ -163,6 +163,7 @@
   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
@@ -421,3 +422,14 @@
 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