| Previous changeset 18:8635a4cee6dd (2017-11-09) |
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Commit message:
add boxplot for per base sequence quality |
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modified:
fastqc_report.Rmd fastqc_report.xml fastqc_report_render.R |
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| diff -r 8635a4cee6dd -r 8c79e5b7cfc0 fastqc_report.Rmd --- a/fastqc_report.Rmd Thu Nov 09 09:22:09 2017 -0500 +++ b/fastqc_report.Rmd Thu Nov 09 09:49:46 2017 -0500 |
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| @@ -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 |
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| diff -r 8635a4cee6dd -r 8c79e5b7cfc0 fastqc_report.xml --- a/fastqc_report.xml Thu Nov 09 09:22:09 2017 -0500 +++ b/fastqc_report.xml Thu Nov 09 09:49:46 2017 -0500 |
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| @@ -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> |
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| diff -r 8635a4cee6dd -r 8c79e5b7cfc0 fastqc_report_render.R --- 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 |
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| @@ -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 ============== |