> On Nov 2, 2017, at 9:27 AM, Ed Siefker <ebs15...@gmail.com> wrote:
>
> 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?
`ggplot` creates an object. You need to print it when used inside a function.
Inside a function (in a more restricted environment) there is no
parse-eval-print-loop.
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
'Any technology distinguishable from magic is insufficiently advanced.'
-Gehm's Corollary to Clarke's Third Law
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