Create Markdown consolidating DESeq treatment vs control analysis

Commit: https://bitbucket.org/mdavis4290/molly-flavonoid-rnaseq/commits/be1ab0f595273dab8b5599f234fd6b2359eb3794

Comments:

• Need help with writing results of 'res05' from each data frame.
• Couldn't show code for knitted PDF file for each analysis due to DESeq adding unwanted comments. I used {r include=FALSE}

  in each chunk to avoid the problem. but like I said it also removes the code from the knitted PDF output.

Attn: [~aloraine]

Cosmetic changes to volcano plots:

I went ahead and made some changes to the volcano plots. I made the x-axis the same for each plot so there are no outliers. The x-axis is -10 and +10 now. The figures are also all squares looking instead of rectangular. The colors are color blind safe and everything should be in one pdf to view. I also made the titles more simple and removed the grid lines so reading the DE genes is easier.

Anthony Response:

Molly,

These look great! Thank you so much for working so quickly! I think these suffice all our requests!

Branch: https://bitbucket.org/mdavis4290/molly-flavonoid-rnaseq/branch/IGBF-3355b

Question for [~molly]:

The commits modify or create several files. Are these commits new? What needs to be merged?

Branch: https://bitbucket.org/mdavis4290/molly3-flavonoid-rnaseq/branch/IGBF-3355
Pull Request: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/20

Notes: Dr. Loraine already review the cosmetic changes to the volcano plots and markdown. The merge should only add:
Knitted markdown: FindControlVsStressDEGenes-DESeq.pdf
Markdown: FindControlVsStressDEGenes-DESeq.Rmd
Figures: Muday-144-Combined-Volcano-Plots.pdf

Merged and ready for testing.

I went ahead and pulled the new commits and pushed them to my branch. I was able to open the markdown and knit the file with no issues. The figures were also fine and had no errors. Can be moved to done or also be reviewed by someone else! Thanks!

[~aloraine]

To test, try to re-compile the knitted version, i.e., make sure it can run on your system.

• Install RStudio and R for your platform
• Request that your bitbucket account be added to Bitbucket workspace https://bitbucket.org/hotpollen, required to access the code repository, which is private
• After getting added to the workspace, clone repo https://bitbucket.org/hotpollen/flavonoid-rnaseq onto your local (note that you can't access the repo until your bitbucket identity is added to the "hotpollen" group on bitbucket)
• Once the repo is cloned onto your local computer, start RStudio and use it to open project directory 72_F3H_PollenTube (you can probably also just double-click file 72_F3H_PollenTube.Rproj to open the rpoject)
• Within RStudio, open file Muday-DESeq-PCA-Plots.Rmd
• Proceed with any prompts from RStudio to install dependencies needed to "knit" (compile) the file Muday-DESeq-PCA-Plots.Rmd. RStudio will likely ask you to install "knitr", the .Rmd file compiler
• Once knitr is installed, run "knitr" by clicking the ball of yarn icon or using the appropriate RStudio menus
• Observe that the first time you try to run the code, RStudio should automatically download and install dependencies required by the code, such as various Bioconductor libraries for analyzing RNA-Seq data, etc. You may need to run knitr more than once. This is normal.
• Observe that if the code runs properly, a file named Muday-DESeq-PCA-Plots.pdf should be created.

Question for [~molly]:

• I just noticed that the knitted version of Muday-DESeq-PCA-Plots.Rmd is not version-controlled in the repository. Is this intentional?

Answer: MD waiting to commit the knitted version pending editing / re-writing the .Rmd file.

The file knits and a PDF is created. Moving to Done.