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Ever set verbose = FALSE thinking it just quiets down your code?

That's true — but it can do so much more.

Here's how understanding verbose gave me full control over function output — and can help you debug smarter too.

🧵 1/ Let’s start with the basics:

verbose controls how much info a function prints as it runs.

Most people only use:

verbose = TRUE  # Show messages
verbose = FALSE # Be silent

But here’s what many miss 👇

2/ Numeric levels for more control

In many R functions, verbose can take numeric levels like 0, 1, 2, or 3.

Think of it like choosing the volume of commentary your function gives.

3/ 🎚️ Verbose Levels Explained:

• 0 → 🔇 Silent (no messages)
• 1 → ✅ Basic updates (default when TRUE)
• 2 → 🧐 Intermediate detail (e.g., filtering steps, loop progress)
• 3 → 🔍 Full debugging mode (internal messages, diagnostics)

4/ Example:

myFunction(data, verbose = 0) # quiet
myFunction(data, verbose = 1) # normal messages
myFunction(data, verbose = 2) # detailed logs
myFunction(data, verbose = 3) # debug everything

This is useful for testing, pipelines, or debugging complex steps.

5/ 📦 In packages like WGCNA:

verbose isn't capped. You can set:

verbose = 4, 5, 6…even 7+

These unlock:

• Correlation and model fit info
• Diagnostic stats
• Matrix dimensions
• Time taken for each power

sft = pickSoftThreshold(datExpr, powerVector = 1:20, verbose = 5)

Note: verbose is not standardized — each function can implement it differently.

6/ 🔬 What about Seurat?

Functions that support verbose = TRUE:

NormalizeData()
ScaleData()
RunPCA()
FindNeighbors()
FindClusters()
RunUMAP()

These show status updates unless you mute them.

7/ ❌ Functions without verbose:

AverageExpression()
FetchData()
DimPlot()

No toggle — they just run silently.

💡 Tip: Unsure if a function supports verbose? Try:

args(FunctionName)
# or
?FunctionName

8/ 🧠 Analogy: Verbose is like a car dashboard

• 0 = No display — flying blind
• 1 = Speed only
• 2 = Add fuel + RPM
• 3 = Every warning light flashing

You decide how much feedback you want.

9/ ✅ Key takeaways:

• verbose isn't just TRUE/FALSE — it can be granular
• Great for debugging, loops, batch workflows
• Helps trace what's going on under the hood

Ever used verbose = 2 or 3 in your code? What's your go-to level?

#RStats #Bioinformatics #Debugging #DataScience