16 May 2014

ddRADseq, LaTex, Silene, git, and rmarkdown

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May 12 - 16 notes

2014-05-12

ApTranscriptome

Finished plotting when expression increases or decreases. Significant differences between colonies, but is it biologically meaningful?

• R with Hadoop
• AN practice talk
• Gotelli lab clean-up

ddRADseq

SHC ran PCR on samples with varying amounts of adapters from ligation step. Worked! Looks like adapter concentration was too low in ligation step and required empirical determination.

Reading

Eckert, A.J., Bower, A.D., Wegrzyn, J.L., Pande, B., Jermstad, K.D., Krutovsky, K.V., Clair, J.B.S. & Neale, D.B. (2009). Association Genetics of Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-Hardiness Related Traits. Genetics, 182, 1289–1302.

Eckert, A.J., Wegrzyn, J.L., Liechty, J.D., Lee, J.M., Cumbie, W.P., Davis, J.M., Goldfarb, B., Loopstra, C.A., Palle, S.R., Quesada, T., Langley, C.H. & Neale, D.B. (2013). The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae). Genetics, 195, 1353–1372.

Walsh, B. & Blows, M.W. (2009). Abundant Genetic Variation + Strong Selection = Multivariate Genetic Constraints: A Geometric View of Adaptation. Annual Review of Ecology, Evolution, and Systematics, 40, 41–59.

Yin, T., Cook, D. & Lawrence, M. (2012). ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biology, 13, R77.

2014-05-13

• Web app for writing LaTex
• Udacity course on Exploratory Data Analysis in R
• R quirks
  • to keep a single row of a matrix as a matrix use dim(mymatrix[1, , drop = F])
• Watermark images using ImageMagick

• Create animated GIF using ImageMagick

  convert -delay 500 -loop 0 ant_field_trip.Joshua_Brown.7.13_25_of_38.jpg Cf.jpeg aphaeno_mollybog_20130515.png ant_field_trip.Joshua_Brown.7.13_15_of_38.jpg Cf_greenhouse.jpg ant_field_trip.Joshua_Brown.7.13_36_of_38.jpg JSG_animation.gif

Silene

Finished tech report - sent to Steve

ApTranscriptome

Writing…

2014-05-14

• Citable DOI for Github repository!

ApTranscriptome

Changed manuscript document to be compatible with the rmarkdown package. Added YAML header:

and can now compile PDF with citations directly from RStudio! In theory, can also do from command-line using Rscript -e "library(knitr); library(rmarkdown); render('input.Rmd')" though I haven’t tested this.

2014-05-16

Analysis. Writing. Getting there!!!

• Include git version information as watermark in LaTex. Cool!