Support `edit()` similar to RStudio

[sher-l]

System details:

Positron and OS details:

version: Positron Version: 2025.06.0 (system setup) build 167
Code - OSS Version: 1.100.0
Commit: e7e5d55
Date: 2025-05-29T21:27:54.586Z
Commit: 34.5.1
Date: 132.0.6834.210
Electron: 20.19.0
ElectronBuildId: 13.2.152.41-electron.0
Chromium: Windows_NT x64 10.0.19045

Describe the issue:

R 4.2.3 Seurat 5.1.0

When I try to modify Seurat's internal functions using edit.

DoHeatmap1 <- edit(Seurat::DoHeatmap())
Error in DefaultAssay():
! argument "object" is missing, with no default
Hide Traceback
▆

1. ├─utils::edit(Seurat::DoHeatmap())
2. └─Seurat::DoHeatmap()
3. ├─assay %||% DefaultAssay(object = object)
4. └─SeuratObject::DefaultAssay(object = object)

Even if I directly copy the DoHeatmap function content and reassign it to DoHeatmap1, it still doesn't work like in RStudio and throws an error.

Error in Melt():
! could not find function "Melt"
Hide Traceback
▆

1. └─global DoHeatmap1(...)
2. └─global SingleRasterMap1(...)

Expected or desired behavior:

Please provide F2 and edit functionality similar to RStudio, or if it already exists, please let me know where to find it.

[sharon-wang]

Hi @sher-l!

The RStudio F2 experience should be available in Positron as long as RStudio keybindings are enabled in Positron.

Could you please check your Positron settings to see if workbench.keybindings.rstudioKeybindings is enabled? If it isn't, you'll need to enable that setting and restart Positron before the keybindings kick in.

Please give this a try and let us know if the behaviour is what you're looking for!

[jennybc]

Side observation about something that might be complicating this discussion:

utils::edit(Seurat::DoHeatmap())

Shouldn't that be utils::edit(Seurat::DoHeatmap)? As in, you want to refer to Seurat::DoHeatmap instead of invoking it?

[jennybc]

I am reading up on RStudio's F2 right now for migration docs and I think this is likely what OP is getting at:

It is possible to navigate to both user-defined own functions (defined in R source files) and any other function defined within an R package. For functions defined within packages, the code is displayed in a special Source Viewer pane, which is read-only.

I suspect this is about functions whose definition is not "in scope", e.g. it's from an installed package, not the user's code.

[lionel-]

Regarding "Go to definition" (F2 in RStudio, F12 in Positron), we could possibly use View() as a fallback when a static definition is not known. I've written about this here: #8632.

Regarding edit(), it's an RStudio feature I did not know about. It allows you to edit a function in an editor. Once the editing is done and the changes are saved, edit() returns with an updated R object (in this case a function). So you can do updated <- edit(identity). Note the object is not modified in place (which is good!).

Screen.Recording.2025-07-23.at.14.34.57.mov

I tried to edit a data frame and it opened an X11 window with a base R implementation of a spreadsheet. After saving changes, the updated data frame is returned. We could potentially hook that up to the data viewer if it allows changing data.

Screen.Recording.2025-07-23.at.14.36.50.mov