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.
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)
ggplot(...) + geom_whatever1(...) +
geom_whatever2(...) +
stat_whatever3(...) +
geom_title(...) + scale_y_log10(...)
Error in "+ geom_whatever2(...) invalid argument to unary operator"
cf. answer to "Split code over multiple lines in an R script"
Try to consolidate the syntax in a single line. this will clear the error
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.
Source: Stackoverflow.com