Installing biopalette

Requirements

biopalette requires R 4.1 or later. It works on Windows, macOS, and Linux and does not contain compiled code.

The package uses four runtime dependencies:

  • cli for user-facing messages;
  • ggplot2 for previews, galleries, and scales;
  • jsonlite for reading and writing palette collections;
  • scales for continuous color interpolation.

R installs these dependencies automatically when biopalette is installed.

Install from CRAN

Install the current release from CRAN:

install.packages("biopalette")

Install from GitHub

The development version is available from GitHub. Install it when you need a feature or fix that has not yet reached CRAN. We recommend pak because it resolves dependencies and reports installation problems clearly.

install.packages("pak")
pak::pkg_install("evanbio/biopalette")

Alternatively, install with remotes:

install.packages("remotes")
remotes::install_github("evanbio/biopalette")

You only need to install pak or remotes once.

Verify the installation

Load the package, inspect its version, and list a few bundled palettes:

library(biopalette)

packageVersion("biopalette")
#> [1] '0.2.2'
head(list_palettes()[c("name", "type", "n_color")])
#>            name      type n_color
#> 1  bcell_atlas2 diverging       5
#> 2     clone_age diverging       5
#> 3  clone_memory diverging       5
#> 4 ppi_transient diverging       5
#> 5  walter_white diverging       5
#> 6 walter_white3 diverging       5

For a visual check, open the palette gallery in an interactive R session:

palette_gallery()

Update

Run the same GitHub installation command to update to the latest development version:

pak::pkg_install("evanbio/biopalette")

Restart R after updating if biopalette was loaded in the current session. This ensures that R uses the newly installed namespace and package files.

Troubleshooting

R cannot install a dependency

Start a fresh R session and retry the installation. If the error identifies a specific dependency, install that package directly to expose its complete error message:

install.packages("packageName")

biopalette itself does not require compilation. On Windows, Rtools is needed only when R must install a dependency from source and that dependency contains compiled code. Install the version of Rtools that matches your R version if the error explicitly says that build tools are required.

GitHub cannot be reached

Confirm that the repository is accessible in a web browser and that R can connect to GitHub. On managed institutional networks, use the proxy or certificate settings supplied by your system administrator; do not place credentials in scripts committed to version control.

R loads an older version

Check the installed version and library location:

packageVersion("biopalette")
find.package("biopalette")
.libPaths()

Multiple R libraries can contain different copies of the package. Remove the older copy from the library reported by find.package() or install the update into that library.

Uninstall

remove.packages("biopalette")

If more than one library contains biopalette, pass the relevant library path through the lib argument of remove.packages().

Where to begin

After installation:

  • open vignette("get-started", package = "biopalette") for the core R workflow;
  • open vignette("palette", package = "biopalette") to browse the palettes included with the package;
  • open vignette("tessera", package = "biopalette") to continue from palette discovery to example data and complete R figure recipes.

Getting help

When reporting an installation problem, include the complete error message and the output of sessionInfo(). Remove tokens, passwords, user names, and other sensitive paths before posting the output publicly.