Skip to content

Fix VM setup issues: WebGestaltR/cargo, ggridges #38

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
hosseinvk merged 1 commit into from
Aug 10, 2026
Merged

Fix VM setup issues: WebGestaltR/cargo, ggridges #38

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions 01-02-setup.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ install.packages(c(
"gprofiler2",
"ggupset",
"ggtangle",
"ggridges", # needed by enrichplot::ridgeplot()
"msigdbr",
"ontologyIndex",
"WebGestaltR",
Expand All @@ -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")`.

<p>&nbsp;</p> <!-- insert blank line -->

## Bioconductor packages
Expand Down
2 changes: 2 additions & 0 deletions 08-2-stringdb.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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`.
Expand Down
Loading