[R] ggplot inside function doesn't plot

[David Winsemius]

> On Nov 2, 2017, at 9:27 AM, Ed Siefker <ebs15242 at 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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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law