Interactive Sessions 10

Updating our R packages, {kable} tables, and a first git collaboration

1. Setup

  • Create new repo on GitHub named eds221-day10-comp
  • Clone to make a local version-controlled R Project

2. Make a ggplot theme

  • Add a new Quarto document, saved in your project root as my_ggplot_theme.qmd
  • Attach the tidyverse and palmerpenguins packages
  • Create a plot from the data (whatever type you want)
  • Highly customize the theme() component (you can make it as bright / awful as you want - this is going to become a ggplot theme you can share with the world, so it’s up to you)
  • Keep this project OPEN (you’ll copy your custom theme in the next step…)

Here’s something awful just to remind you of what this can look like:

ggplot(data = penguins, aes(x = flipper_length_mm, y = body_mass_g)) +
  geom_point() +
  theme(title = element_text(size = 16, color = "purple"),
        plot.background = element_rect(fill = "black"),
        panel.background = element_rect(fill = "gray20"),
        axis.text = element_text(color = "yellow"),
        panel.grid.major = element_line(color = "blue"),
        panel.grid.minor = element_line(color = "cyan")
        )

3. Making some nice tables in R

We’ve made a number of ggplot graphs, but we haven’t made any tables. Let’s learn one way!

  • Back in your eds221-day10-comp R Project, create a new Quarto document
  • In the setup chunk, attach the tidyverse & kableExtra (note: there are a bunch of ways to make nice tables in R - see David Keyes’ post on How to make beautiful tables in R for more options)
  • Copy the contents of the table below to the clipboard, the use the datapasta Add-in to create a tibble stored as whale_sightings
date site spp dist_m behavior
8/12/2014 channel unknown 400 breach
8/13/2014 channel gray 200 spout
8/15/2014 harbor gray 60 spout
8/16/2014 channel humpback 300 feeding
8/16/2014 channel gray 150 feeding

Let’s make some nice looking tables

With kableExtra:

# Bootstrap theme
dt %>% 
  kable(col.names = c("Date", "Site", "Species", "Distance (m)", "Behavior")) %>% 
  kable_styling(full_width = FALSE, bootstrap_options = "striped")
Date Site Species Distance (m) Behavior
8/12/2014 channel unknown 400 breach
8/13/2014 channel gray 200 spout
8/15/2014 harbor gray 60 spout
8/16/2014 channel humpback 300 feeding
8/16/2014 channel gray 150 feeding 
# Paper theme
dt %>% 
  kable() %>% 
  kable_classic()
date site spp dist_m behavior
8/12/2014 channel unknown 400 breach
8/13/2014 channel gray 200 spout
8/15/2014 harbor gray 60 spout
8/16/2014 channel humpback 300 feeding
8/16/2014 channel gray 150 feeding

Check out some other themes and try them out! https://cran.r-project.org/web/packages/kableExtra/vignettes/awesome_table_in_html.html

A bit more customization:

dt %>% 
  kable(col.names = c("Date", "Site", "Species", "Distance (m)", "Behavior")) %>% 
  kable_classic() %>% 
  column_spec(1, bold = TRUE, background = "yellow") %>% 
  column_spec(2, italic = TRUE, background = "orange") %>% 
  add_header_above(c(" " = 1, "One header" = 2, "Another header" = 2)) %>% 
  scroll_box(height = "100px", width = "500px")
One header
Another header
Date Site Species Distance (m) Behavior
8/12/2014 channel unknown 400 breach
8/13/2014 channel gray 200 spout
8/15/2014 harbor gray 60 spout
8/16/2014 channel humpback 300 feeding
8/16/2014 channel gray 150 feeding

See also: DT, reactable, gt, and more!

4. Git collaboration: both pushing to main

  • Find a partner. Designate who is “Starter” and who is “Collaborator”.

Starter: Create a new version controlled R Project, make & push an update

  • Create a new repo called eds221-day10-collab (with a ReadMe)
  • Clone, create a new version-controlled R Project
  • Create a new .Rmd in the root (git_test.Rmd), delete everything below the first code chunk
  • Add a line of text in your .Rmd like “Hi partner!”
  • Stage, commit & push all changes back to your GitHub repo

Starter: Add a contributor

  • Go back to your eds221-day10-collab repo on GitHub
  • Go to Settings > Manage access > (Enter password if requested) > Invite collaborator > Enter Collaborator’s username or email

Collaborator: Accept invitation & clone repo, make an update

  • Check your email. You should receive the invitation to join the repo. Accept.
  • Clone (do NOT fork first) and create your own local R project
  • Pull just in case (this should say already up to date)
  • Open the git_test.Rmd
  • Add a new line to the .Rmd with a nice note below the line your partner added
  • Save the .Rmd, then stage, commit, pull & push
  • Check that the updates show up on GitHub

Starter: Pull & add something new to the .Rmd

  • PULL to get remote updates locally in RStudio
  • Open git_test.Rmd and see updated text from your partner
  • Add a new line of text to the .Rmd
  • Stage, commit, pull, then push

Collaborator: Pull & add something new to the .Rmd

  • PULL to get remote updates
  • Open git_test.Rmd and see updated text
  • Add a new line of text to the .Rmd
  • Stage, commit, pull, then push

Where goes what now on GitHub?

  • Both partners, go back to the repo on github for your collaboration
  • Go exploring (especially History & Blame)

Submit a new issue that references specific line(s) in your files

  • Still in GitHub, click on the git_test.Rmd file
  • Find a line that your partner wrote
  • Click the row number to the left of the line (or hold shift to select a range a lines) - the selected lines will turn yellow, and you should see a three dot menu button appear to the left of the code. Click on it, and choose “Reference in new issue”
  • Add a title and some text for your issue, and submit
  • Once you both have submitted an issue to your shared repo, check your partner’s issue, respond and close (resolve) the issue

End Interactive Session 10