Use Claude Code for R in VS Code on Mac

You’ve set up R in VS Code and can write code manually. Now you want AI to help write, improve, and debug your R code while you focus on the analysis. Think of Claude Code as a coding partner who lives inside VS Code - you describe what you want, and it writes or improves the code while you stay in the same window.

Key Concepts

Claude Code Extension - VS Code extension that brings Claude AI assistant directly into your editor with inline code edits
Chat Panel - Side panel in VS Code where you converse with Claude about your code
Inline Edits - Claude’s suggested code changes appear directly in your files with diffs you can accept or reject

What You’ll Need

Finished R in VS Code tutorial - R should be working in VS Code
Finished Installing Claude Code on Mac tutorial - Claude Code CLI should be installed
A paid Claude plan (such as Pro or Max) or an Anthropic Console account — the free plan doesn’t include Claude Code
20-30 minutes

Step 1: Open VS Code and Create R Project

Open Visual Studio Code
Click File in the menu bar, then Open Folder
Navigate to your Documents folder
Click New Folder at the bottom of the dialog
Name the folder claude_r_test
Click Open to open the new folder
If prompted “Do you trust the authors?”, click Yes, I trust the authors

Click the Extensions icon in the left sidebar (four squares icon)
In the search box, type Claude Code
Find Claude Code for VS Code by Anthropic and click Install
After installation, click ✻ Claude Code in the status bar at the bottom-right of the window to open the Claude panel (once a file is open, you can also use the Spark icon at the top-right of the editor)
Click Sign in and finish signing in with your Claude account in the browser that opens
If you use an API key instead, set it up as shown in Installing Claude Code on Mac (Step 3, Option B), then quit VS Code and open it again
Once signed in, you’ll see a Learn Claude Code checklist. You can close it with the X

Step 3: Create Initial R Script Manually

Click File > New File… in the menu bar
In the list that appears at the top of the window, choose R Document
Save the file by clicking File > Save, name it iris_analysis.R
Type this code:

data(iris)
str(iris)
summary(iris)

Save the file by clicking File > Save
Open R terminal: click View in menu bar, then Command Palette, type R: Create R Terminal, press Enter
Select the code and press Ctrl+Enter (Windows/Linux) or Cmd+Enter (Mac) to run it
You should see dataset structure and summary statistics in the terminal

Step 4: Ask Claude to Add Scatter Plot

Click the Spark icon at the top-right of the editor (or ✻ Claude Code in the status bar) to open the Claude panel
In the chat box at the bottom, type:

Add code to iris_analysis.R to create a scatter plot of sepal length vs. width, colored by species. Use ggplot2.

Press Enter to send
Claude reads your file and edits it - the new code appears in iris_analysis.R
If Claude shows a diff and asks for permission, accept the change
The ggplot2 code appears in your file
If you don’t have ggplot2 installed, run install.packages("ggplot2") in the R terminal

Step 5: Run the Updated Code

Select all code in iris_analysis.R
Press Ctrl+Enter (Windows/Linux) or Cmd+Enter (Mac)
A scatter plot appears in a plot tab inside VS Code
You should see points colored by species (setosa, versicolor, virginica)

Step 6: Ask Claude to Refine Plot

In the Claude chat panel, type:

Remove title. Change marker type by species. Change to the classic theme.

Press Enter
Claude shows the updated code changes
If asked, accept the change
Run the updated code again: select all and press Ctrl+Enter / Cmd+Enter
The plot now displays with different marker shapes per species, no title, and classic theme

Step 7: Ask Claude for PCA Analysis

In the Claude chat panel, type:

Add code to perform PCA on the numeric variables and plot the samples using the first two principal components.

Press Enter
Claude adds PCA code to your script
If asked, accept the change
Run all code: select all and press Ctrl+Enter / Cmd+Enter
A PCA plot appears showing samples projected onto PC1 and PC2, colored by species

Step 8: Ask Claude to Review and Comment

In the Claude chat panel, type:

Review the entire script for correctness. Add comments when necessary.

Press Enter
Claude reviews the code and suggests comments explaining each section
If asked, accept the change
Your script now has clear comments explaining the data loading, visualization, and PCA analysis

Next Steps

Ask Claude to create an R Markdown report: “Create an R Markdown file for this analysis”
Use Claude to debug errors: “This code gives Error X, can you fix it?”
Request statistical tests: “Add a t-test comparing sepal length between setosa and versicolor”
Ask Claude to optimize code: “Make this loop faster using vectorization”
Get help with unfamiliar functions: “Explain what dplyr::mutate does”

Troubleshooting

Claude extension not showing - Restart VS Code after installation. Click View > Extensions to verify it’s installed.
“Cannot read R file” error - Make sure you saved the file with .R extension. Claude needs saved files to read them.
Authentication failed - Verify your paid Claude plan or Anthropic Console account is active. See Installing Claude Code on Mac for authentication troubleshooting.
ggplot2 not found - Install it in R terminal: install.packages("ggplot2"). Wait for installation to complete before running code.
Code changes not applying - If Claude asked for permission, make sure you accepted the change. If it’s not working, try copying Claude’s suggested code manually.

Workflow Summary

Claude Code Extension provides an AI assistant directly in VS Code with chat panel and inline diffs
Iterative refinement - Start with basic code, ask Claude to enhance, test immediately, then refine further
Context awareness - Claude reads your R files and understands your project structure
Inline editing - Proposed changes appear as diffs in your actual files, not separate chat responses
Stay in flow - No switching between browser and editor - everything happens in VS Code

Created by Steven Ge on December 11, 2025.