I have a function:
myplot <- function (X) {
d <- plotCounts(dds2, gene=X, intgroup="condition", returnData=TRUE)
png(paste("img/", X, ".png", sep=""))
ggplot(d, aes(x=condition, y=count, color=condition)) +
geom_point(position=position_jitter(w=0.1,h=0)) +
scale_y_log10(breaks=c(25,100,400)) +
ggtitle(X) +
theme(plot.title = element_text(hjust = 0.5))
dev.off()
}
'd' is a dataframe
count condition
E11.5 F20HET BA40_quant 955.9788 E11.5 F20HET
E11.5 F20HET BA45_quant 796.2863 E11.5 F20HET
E11.5 F20HET BB84_quant 745.0340 E11.5 F20HET
E11.5 F9.20DKO YEH3_quant 334.2994 E11.5 F9.20DKO
E11.5 F9.20DKO fkm1_quant 313.7307 E11.5 F9.20DKO
E11.5 F9.20DKO zzE2_quant 349.3313 E11.5 F9.20DKO
If I set X="Etv5" and paste the contents of the function into R, I get
'img/Etv5.png'
If I run myplot(X), I get nothing.
> X
[1] "Etv5"
> list.files("img")
character(0)
> myplot(X)
null device
1
> list.files("img")
character(0)
> d <- plotCounts(dds2, gene=X, intgroup="condition", returnData=TRUE)
> png(paste("img/", X, ".png", sep=""))
> ggplot(d, aes(x=condition, y=count, color=condition)) +
+ geom_point(position=position_jitter(w=0.1,h=0)) +
+ scale_y_log10(breaks=c(25,100,400)) +
+ ggtitle(X) +
+ theme(plot.title = element_text(hjust = 0.5))
> dev.off()
null device
1
> list.files("img")
[1] "Etv5.png"
Why doesn't my function work?
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