Getting a human body silhouette in svg format...

Well Wikipedia is clearly a good option...

Various types available...

https://commons.wikimedia.org/wiki/File:Human_body_silhouette.svg
https://commons.wikimedia.org/wiki/File:Female_shadow.svg
https://commons.wikimedia.org/wiki/Category:SVG_human_body_features
https://commons.wikimedia.org/wiki/Category:Diagrams_of_the_human_body_features
https://commons.wikimedia.org/wiki/Category:Diagrams_of_the_human_anatomy
https://commons.wikimedia.org/wiki/Category:Diagrams_of_organs_of_the_human_body




R packages
https://cran.r-project.org/web/packages/rcorpora/rcorpora.pdf
has a body part list: https://github.com/dariusk/corpora/blob/master/data/humans/bodyParts.json

R Shiny app
https://sidderb.wordpress.com/2013/01/30/a-shiny-app-to-display-the-human-body-map-dataset/


Websearch reveals these questions:
https://stackoverflow.com/questions/10670751/r-plot-human-body-in-2d

https://stackoverflow.com/questions/28664798/how-to-make-a-heat-map-in-r-based-on-a-gif-of-the-human-body

https://stackoverflow.com/questions/4993189/overlay-data-onto-background-image

https://stackoverflow.com/questions/16409935/plot-data-over-background-image-with-ggplot/16418186#16418186

https://stackoverflow.com/questions/24839363/how-to-use-more-than-6-shapes-in-ggplot

development packages page for Bioconductor

So here is the development packages page for Bioconductor

http://bioconductor.org/packages/devel/bioc/

I guess drawProteins should be here soon...

I think this code should install development version from Bioconductor when it's there:

install.packages("drawProteins",
 repos = "http://www.bioconductor.org/packages/devel/bioc",
     type  = "source")

I will check back and test it in a few days...

N.B. Will it work?

For the development version on github:

Merging a branch using git desktop...

learning from here: https://git-scm.com/book/en/v2/Git-Branching-Basic-Branching-and-Merging
Seems to make sense to update devel branch from master first...

This worked.

Also both master and devel branch pass build on Travis - GOOD!


Now try to merge branch....

https://www.attosol.com/create-and-merge-branches-using-github-desktop-client/

tells us to Create a Pull Request

Then:
Compare
Update
Sync

Not doing this but I should...

https://www.bioconductor.org/developers/how-to/useDevel/

Addressing comments from Bioconductor...

A few relatively minor comments:

"Looks good. Just a couple of comments -

1. LazyData: true
   Any particular reason why you're setting this to 'true'? I ask because we've seen this cause problems (long delays) when loading packages with substantial data. My recommendation would be to leave this as 'False'.
2. Both httr and ggplot2 are imported in DESCRIPTION. They should be selectively or fully imported in the NAMESPACE."

from: https://github.com/Bioconductor/Contributions/issues/541

Changing LazyData: false means adding data() functions before each command in examples as mentioned here: http://kbroman.org/pkg_primer/pages/data.html

No good reason not to do this so - DONE. 

Using the Roxygen tags to @import ggplot2 and @import httr at the appropriate times changes the NAMESPACE in the appropriate way. 

Advice here:

• http://r-pkgs.had.co.nz/namespace.html
• https://cran.r-project.org/web/packages/roxygen2/vignettes/namespace.html
• https://stackoverflow.com/questions/8597993/does-roxygen2-automatically-write-namespace-directives-for-imports-packages

Once, I worked out how to do this - DONE. 

So basically all done - testing and version bumping required. 

Learning more about git: Reverting a commit...

Within github,
     I want to try reverting to a version of drawProteins that passed build...

So the reversion seems to have worked.

Bumped to 0.99.5 to try to get a new build... don't know if it will be enough...

Currently being tested on Bioconductor and Travis... time for a cup of tea.
currently 13:54


So now I have created a branch in Github Desktop

However, how do I know I'm working on a branch?



So within Git Desktop there is the option to commit to 'master' or 'branch'

Great.
And there was a publish button at one point.
FROM NOW ON: only commit to devel until it works and builds - need separate build process, I think....

Travis will build automatically which is good.

Trying to open Raspberry Pi SD card on a mac...

Tried: 

https://www.engadget.com/2009/09/07/how-to-set-up-ubuntu-linux-on-a-mac-its-easy-and-free/

creating a Virtual Box

Downloaded ISO file from here:

https://www.raspberrypi.org/downloads/raspberry-pi-desktop/

This worked and gave me a nice raspberry pi version on the mac - very useful. 

But still can't access the SD file...

This advice would be good but I can't really understand it...

https://www.engadget.com/2009/09/07/how-to-set-up-ubuntu-linux-on-a-mac-its-easy-and-free/