Making your plots interactive - update

Two years ago I have been experimenting with Shiny and interactive plots and I have published here a post that remains to be one of the most read pages of this blog. I feel guilty about it because I was wrong about almost everything. A few weeks later, the free use of shinyapps.io was over. Meanwhile, plotly package, I did not appreciate that time so much, has matured and added more R functionality.

If you are into ggplot2, it is now super-easy to add interactivity to your graph. Just take your static ggplot object pl like the following

mpg dataset

and run

library(plotly)
ggplotly(pl)

That's it. You can configure your tooltip text with ggplotly(pl, tooltip = "text"), see my Rmarkdown example. And it works not only for a simple scatterplot but for more complex graphs as well, as @cpsievert tweeted today.

I made @galka_max Europe map interactive with 2 more lines of #rstats code https://t.co/KZp0w5YoFH pic.twitter.com/a4GaFJRJVn

— Carson Sievert (@cpsievert) April 26, 2017

There are now also many easy-to-use htmlwidgets. And with the ggiraph package, you get now your click as Shiny input.

Teaching R course? Use analogsea to run your customized RStudio in Digital Ocean!

Two years ago I taught an introductory R/Shiny course here at The Jackson Lab. We all learnt a lot. Unfortunately not about Shiny itself, but rather about incompatibilities between its versions and trouble with its installation to some machines.

And it is not only my experience. If you look into forums of Rafael Irizarry MOOC courses, so many questions are just about installation / incompatibilities of R packages. The solution exists for a long time: run your R in a cloud. However, customization of virtual machines (like Amazon EC2) used to be a nontrivial task.

In this post I will show how a few lines of R code can start a customized RStudio docklet in a cloud and email login credentials to course participants. So, the participant do not need to install R and the required packages. Moreover, it is guaranteed they all run exactly the same software. All they need is a decent web browser to access RStudio server.

RStudio server login

Running RStudio in Digital Ocean with R/analogsea

So how complicated is it today to start your RStudio on clouds? It is (almost) a one-liner:

1. If you do not have  Digital Ocean account, get one. You should receive a promotional credit $10 (= 1 regular machine running without interruption for 1 month):
   https://www.digitalocean.com/
   (full disclosure: if you create your account using the link above I might get an extra credit)
2. Install analogsea package from Github. Make sure to create Digital Ocean personal access token and in R set DO_PAT environment variable. Also create your personal SSH key and upload it to Digital Ocean.
3. And now it is really easy:
   
   library(analogsea)
   # Sys.setenv(DO_PAT = "*****") set access token
   
   # start your machine in Digital Ocean
   d <- docklet_create(size = getOption("do_size", "512mb"))
   # run RStudio on machine 'd' (rocker/rstudio docker image)
   d %>% docklet_rstudio()

The last line should open your browser with RStudio login page (user "rstudio", password "rstudio"). If not, use summary(d) to get the IP address of your machine and go to http://your_machine:8787. 

It will cost you ~$0.01 per hour ($5 per month, May 2015). When you are done, do not forget to stop your Digital Ocean machine (droplet_delete(d)). At the end, make sure that you successfully killed all your machines - either log in to Digital Ocean or by calling droplets() in R.

Make your R plots interactive

THIS POST IS NOW OBSOLETE, USE PLOTLY OR GGIRAPH, SEE MY CODE EXAMPLE

As a part of my daily job, I draw scatterplots, lots of them. And because there are thousands of genes expressed in any mouse or human tissue, my typical plot looks something like this (code). (Actually, it is a comparison of variance that can be attributed to "sex" factor in mRNA vs. protein expression.)

The question is - what is a gene in the top right corner? And what is the one next to him? And this one? And that?

Shiny Year 2014

http://glimmer.rstudio.com/simecek/pf2014en/ (source on Github)

"Pour Felicitér" is a French phrase used by Czech and Slovak to wish a happy new year, but not in French speaking countries. It is dating back to the beginning of 19. century when French was popular in Czech/Austrian city population similar way as English is today.

I originally wanted to make it a snow flake to share a plenty of snow we have in Maine. But then I discovered this Xmas R post and made it Shiny.

Let your 2014 be shiny as well!