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
Claude Pro/Max subscription or Anthropic API key
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 by Anthropic and click Install
After installation, a Claude icon (sparkle) appears in the left sidebar
Click the Claude icon to open the chat panel
Click Sign in to Claude Code in the chat panel
Choose your authentication method:
- Claude Pro/Max users: Click Sign in with Claude.ai, authorize in browser, and copy the code back to VS Code
- API key users: Click Use API Key and paste your Anthropic API key
For detailed authentication steps, see the Installing Claude Code on Mac guide (Step 5)
Once signed in, you’ll see “Ready to help” in the chat panel

Step 3: Create Initial R Script Manually

Click File > New File in the menu bar
Click Select a language and type R, then select R
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 Claude icon in the left sidebar to open the chat 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 proposes changes - you’ll see a diff showing new code to add
Click Accept to apply the changes
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 separate graphics window
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
Click Accept
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
Click Accept
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
Click Accept
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 Claude Pro/Max subscription is active or your API key is valid. 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 - Make sure to click Accept on the diff. 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.