A collection of changes for visual improvements

[ycl6]

This PR makes the following changes to the current code base

1. When using number.angles to specify the rotation of the number labels above the bars, angles between 0 and 90 will now place the number in a better position visually [Rotated bar labels off-center #70, number.angles error #78, Plot only n-way intersections, filter out empty intersections, number position above intersections #133]
2. vjust is used to increase the set title (as specify by column) above the heatmap when incorporating set metadata
3. plot_lims is changed to factor to that the boxplot can be properly aligned [Boxplot not align with the main plot #195]
4. changes were makde to replace the deprecated aes_string function and wrong use of size to specify line widths [updates for ggplot2 upgrade? #270]

---

On [1], these are the plots before the changes

upset(movies, number.angles = 0)

upset(movies, number.angles = 45)

upset(movies, number.angles = 90)

---

On [1], these are the plots after the changes

upset(movies, number.angles = 0)

upset(movies, number.angles = 45)

upset(movies, number.angles = 90)

[ycl6]

To install this patch, you can use the remotes::install_github() as below:

# Remove UpSetR
remove.packages("UpSetR")

# Install the `number_angles` patch
remotes::install_github("ycl6/UpSetR@number_angles")

or

# Remove UpSetR
remove.packages("UpSetR")

# Install from PR #271
remotes::install_github("hms-dbmi/UpSetR", ref = remotes::github_pull(271))

[tiekneeshrimp]

Hi @ycl6 ! Thanks so much for updating this! I tried both of these options:

remotes::install_github("hms-dbmi/UpSetR", ref = remotes::github_pull(271))

and

remotes::install_github("ycl6/UpSetR@number_angles")

Both of which resulted in this error:

Error in github_resolve_ref.github_pull(meta$ref %||% ref, meta, host = host,  : 
  Cannot find GitHub pull request hms-dbmi/UpSetR#271
HTTP error 401.
  Bad credentials

[ycl6]

Hi @tiekneeshrimp The error seems to be related to Github PAT (personal access tokens) set up and rate limit is restricting access.

Perhaps looking into your GITHUB_PAT like mentioned here will help?