Selected R resources...

http://docs.ggplot2.org/current/vignettes/extending-ggplot2.html

http://kbroman.org/knitr_knutshell/pages/Rmarkdown.html

https://user2017.brussels/tutorials

Some health data from here:
http://www.publichealthwalesobservatory.wales.nhs.uk/home
inc some Tableau exploration tools:
https://public.tableau.com/profile/publichealthwalesobservatory#!/vizhome/PHOFlocalauthorityandhealthboardtool/Home?:iid&:tabs=no



Is there a way to include/publicise/promote my R training in any of these places?:
http://www.learningandwork.org.uk/
http://thenode.biologists.com/

Geomapping - some interesting links...

https://geographicdatascience.com/


http://www.alex-singleton.com/R-Tutorial-Materials/7-converting-coordinates.pdf


https://www.students.ncl.ac.uk/keith.newman/r/maps-in-r

https://cran.r-project.org/doc/contrib/intro-spatial-rl.pdf

http://stackoverflow.com/questions/24136868/plot-map-with-values-for-countries-as-color-in-r

The package 'leaflet'

The R package leaflet should allow the generation of a javascript object that I could use.

This is relevant to the Electives World Map that needs updating - ideally before Monday!!!!

For extra info: https://rstudio.github.io/leaflet/

API resources

R-bloggers blog piece:
https://www.r-bloggers.com/accessing-apis-from-r-and-a-little-r-programming/



Other access to Uniprot:
http://bioconductor.org/packages/release/bioc/html/UniProt.ws.html



EBI webservices:
http://www.ebi.ac.uk/Tools/webservices/

List of possible API to use...

Search google with API and EBI (european bioinformatics institute)

List of services
http://www.ebi.ac.uk/Tools/webservices/


Protein Data Bank
http://www.ebi.ac.uk/pdbe/pdbe-rest-api
PDBe’s REST API is a programmatic way to obtain information from the PDB and EMDB
3D biomacromolecular structures

Who else uses the REST API

The popular 3D viewer Jmol/JSmol has already integrated the REST API calls for quality and cross-references. Jalview, Coot and CCP4 developers have expressed interest.

Python example: https://github.com/PDBeurope/PDBe_Programming

Proteins API

https://www.ebi.ac.uk/proteins/api/doc/

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx237

Ontology API

https://www.ebi.ac.uk/ols/docs/api

Don't forget:

Uniprot Web services R package:

http://bioconductor.org/packages/release/bioc/html/UniProt.ws.html

Making a small change to github...

Yesterday, Stef Locke, showed me how to make a small change in Github.

Go to the file you want to change:

Press on the pen symbol.

Github will automatically create a fork and show this message:

You’re editing a file in a project you don’t have write access to. Submitting a change to this file will write it to a new branch in your fork brennanpincardiff/praise, so you can send a pull request.


Add the text you want to add...
Complete the Propose File Change format:

Then create "Pull Request":

Done...

I've been practicing on the R package called praise:
https://github.com/rladies/praise/

Data Viz for Medical students...

I am planning to talk to Year 1 Medical students next year about data analysis & visualisation.

I am thinking about a new blog around the subject.

Here are some resources, I have found:

Health Intelligence

Analyzing health data, generating and communicating evidence to improve population health

http://publichealthintelligence.org/content/resources/data-tools

Gov.uk

Visualisations about immunisation

https://www.gov.uk/government/collections/immunisation#infographics