I'm using ggplot2 to do a boxplot comparison of two different species, as indicated by the third column shown below:
> library(reshape2) > library(ggplot2) > melt.data = melt(actb.raw.data) > head(actb.raw.data) region expression species 1 CG -0.17686667 human 2 CG -0.06506667 human 3 DG 1.04590000 human 4 CA1 1.94093333 human 5 CA2 1.55023333 human 6 CA3 1.75800000 human > head(melt.data) region species variable value 1 CG human expression -0.17686667 2 CG human expression -0.06506667 3 DG human expression 1.04590000 4 CA1 human expression 1.94093333 5 CA2 human expression 1.55023333 6 CA3 human expression 1.75800000 However, when I run the following code:
ggplot(combined.data, aes(x = region, y = expression, fill = species)) + + geom_boxplot() + + scale_fill_manual(values = c("yellow", "orange")) + ggtitle("Expression comparisons for ACTB") + theme(axis.text.x = element_text(angle=90, face="bold", colour="black")) I get this error:
> ggplot(actb.raw.data, aes(x = region, y = expression, fill = species)) + + + geom_boxplot() + + + scale_fill_manual(values = c("yellow", "orange")) Error in +geom_boxplot() : invalid argument to unary operator > + ggtitle("ACTB expression in human vs. macaque") Error in +ggtitle("ACTB expression in human vs. macaque") : invalid argument to unary operator > + theme(axis.text.x = element_text(angle=90, face="bold", colour="black")) Error in inherits(x, "theme") : argument "e2" is missing, with no default This also happens when I run using the variable melt.data, for whatever that's worth. Can someone help me fix this? I've run this code successfully before with a different dataset that was formatted identically, and I can't figure out what's going wrong here.
34 Answers
It looks like you might have inserted an extra + at the beginning of each line, which R is interpreting as a unary operator (like - interpreted as negation, rather than subtraction). I think what will work is
ggplot(combined.data, aes(x = region, y = expression, fill = species)) + geom_boxplot() + scale_fill_manual(values = c("yellow", "orange")) + ggtitle("Expression comparisons for ACTB") + theme(axis.text.x = element_text(angle=90, face="bold", colour="black")) Perhaps you copy and pasted from the output of an R console? The console uses + at the start of the line when the input is incomplete.
This is a well-known nuisance when posting multiline commands in R. (You can get different behavior when you source() a script to when you copy-and-paste the lines, both with multiline and comments)
Rule: always put the dangling '+' at the end of a line so R knows the command is unfinished:
ggplot(...) + geom_whatever1(...) + geom_whatever2(...) + stat_whatever3(...) + geom_title(...) + scale_y_log10(...) Don't put the dangling '+' at the start of the line, since that tickles the error:
Error in "+ geom_whatever2(...) invalid argument to unary operator"
And obviously don't put dangling '+' at both end and start since that's a syntax error.
So, learn a habit of being consistent: always put '+' at end-of-line.
cf. answer to "Split code over multiple lines in an R script"
It's the '+' operator at the beginning of the line that trips things up (not just that you are using two '+' operators consecutively). The '+' operator can be used at the end of lines, but not at the beginning.
This works:
ggplot(combined.data, aes(x = region, y = expression, fill = species)) + geom_boxplot() The does not:
ggplot(combined.data, aes(x = region, y = expression, fill = species)) + geom_boxplot() *Error in + geom_boxplot(): invalid argument to unary operator* You also can't use two '+' operators, which in this case you've done. But to fix this, you'll have to selectively remove those at the beginning of lines.
Try to consolidate the syntax in a single line. this will clear the error
