changeset 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

--- a/fastqc_report.xml	Thu Nov 09 09:22:09 2017 -0500
+++ b/fastqc_report.xml	Thu Nov 09 09:49:46 2017 -0500
@@ -104,33 +104,13 @@
             }
         </citation>
         <citation type="bibtex">
-            @misc{highcharter2017,
-            title = {highcharter: A Wrapper for the 'Highcharts' Library},
-            author = {Joshua Kunst},
-            year = {2017},
-            note = {R package version 0.5.0},
-            url = {https://CRAN.R-project.org/package=highcharter},
-            }
-        </citation>
-        <citation type="bibtex">
-            @misc{formattable2016,
-            title = {formattable: Create 'Formattable' Data Structures},
-            author = {Kun Ren and Kenton Russell},
-            year = {2016},
-            note = {R package version 0.2.0.1},
-            url = {https://CRAN.R-project.org/package=formattable},
-            }
-        </citation>
-        <citation>
-            @article{ewels2016multiqc,
-            title={MultiQC: summarize analysis results for multiple tools and samples in a single report},
-            author={Ewels, Philip and Magnusson, M{\aa}ns and Lundin, Sverker and K{\"a}ller, Max},
-            journal={Bioinformatics},
-            volume={32},
-            number={19},
-            pages={3047--3048},
-            year={2016},
-            publisher={Oxford University Press}
+            @Book{ggplot22016,
+            author = {Hadley Wickham},
+            title = {ggplot2: Elegant Graphics for Data Analysis},
+            publisher = {Springer-Verlag New York},
+            year = {2009},
+            isbn = {978-0-387-98140-6},
+            url = {http://ggplot2.org},
             }
         </citation>
     </citations>

--- a/fastqc_report_render.R	Thu Nov 09 09:22:09 2017 -0500
+++ b/fastqc_report_render.R	Thu Nov 09 09:49:46 2017 -0500
@@ -4,11 +4,9 @@
 library(plyr)
 library(dplyr)
 library(stringr)
-library(highcharter)
 library(DT)
 library(reshape2)
 library(plotly)
-library(formattable)
 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
 
 ##============ Sink warnings and errors to a file ==============