CODEWITHSUNDEEP
r
JJS
JJS

Reputation: 326

log scale boxplots in R

For the plots I'm trying to generate, I want to apply log scale to the y axis.

The original code is 

bxp(confSum, main="Mean Coverage Per Exon for Hiseq", ylab="Fold Coverage", 
    las=2, cex.lab=1, cex.axis=0.7,xaxt='n', ann=FALSE)

which works fine but not in log scale.

Based on some information online, I added log="y" to the code, and the pdf it produces just become empty with nothing on it...

Did I make a mistake somewhere?.. How should I fix it for log scale?

Thanks in advance.

Upvotes: 13

Views: 25191

Answers (2)

Marina Vance
Marina Vance

Reputation: 81

I had the same issue. I figured out it was because my dataset had some zero values, so I substituted them for NA and it worked out. It's because boxplot function can't handle plotting the 0 values in the log scale (converges to infinite).

Upvotes: 3

Michele
Michele

Reputation: 8753

> boxplot(decrease ~ treatment, data = OrchardSprays,
+         log = "y", col = "bisque")

Upvotes: 9

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