diff --git a/01-02-setup.Rmd b/01-02-setup.Rmd index 48a4e53..d15a9ad 100644 --- a/01-02-setup.Rmd +++ b/01-02-setup.Rmd @@ -21,6 +21,7 @@ install.packages(c( "gprofiler2", "ggupset", "ggtangle", + "ggridges", # needed by enrichplot::ridgeplot() "msigdbr", "ontologyIndex", "WebGestaltR", @@ -29,6 +30,8 @@ install.packages(c( )) ``` +**Note on `WebGestaltR`:** it includes Rust source code that gets compiled during installation, so a working Rust toolchain (including `cargo`) is required beforehand. If installation fails with a "cargo command is not available" or similar error, install/update Rust via [rustup](https://www.rust-lang.org/tools/install) rather than an older distro-packaged `cargo`, then retry `install.packages("WebGestaltR")`. +
## Bioconductor packages diff --git a/08-2-stringdb.Rmd b/08-2-stringdb.Rmd index d96c243..bdcf5f2 100644 --- a/08-2-stringdb.Rmd +++ b/08-2-stringdb.Rmd @@ -215,6 +215,8 @@ sema3a <- string_db$mp("sema3a") string_db$get_interactions(c(crabp2, sema3a)) ``` +An empty data frame here is expected, not an error: `CRABP2` and `SEMA3A` are not annotated as directly interacting in STRING, so there is no row to return. `get_interactions` only reports edges that exist directly between the queried proteins; it will not tell you about shared partners or indirect paths between them. + ### Interaction partners To retrieve the first-shell interaction partners of one or more proteins from the locally loaded network, use `get_interaction_partners`. The output has the same structure as `get_interactions`.