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Ed Siefker

2017-Nov-02 16:27 UTC

[R] ggplot inside function doesn't plot

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?

PIKAL Petr

2017-Nov-02 16:49 UTC

head link

[R] ggplot inside function doesn't plot

Hi

You have to print it.

just add

print(all ggplot stuff)

inside the function.

Cheers
Petr
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Ed
Siefker
> Sent: Thursday, November 2, 2017 5:27 PM
> To: r-help <r-help at r-project.org>
> Subject: [R] ggplot inside function doesn't plot
>
> 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?
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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David Winsemius

2017-Nov-02 16:54 UTC

head link

[R] ggplot inside function doesn't plot

> 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.

> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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

Ed Siefker

2017-Nov-02 17:03 UTC

head link

[R] ggplot inside function doesn't plot

I don't really understand. I mean, I understand the solution is
print(ggplot(...)).  But why is that required in a function and not at
the console?

Shouldn't I be able to rely on what I do at the console working in a
script?  Is this inconsistent behavior by design?



On Thu, Nov 2, 2017 at 11:54 AM, David Winsemius <dwinsemius at
comcast.net> wrote:>
>> 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.
>
>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> 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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