thr3ads.net - R help - [R] ggplot inside function doesn't plot [Nov 2017]

If this information is useful, please help other people find it:
Share via:

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.
________________________________
Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny
pouze jeho adres?t?m.
Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho
odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho
syst?mu.
Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email
jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat.
Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i
zpo?d?n?m p?enosu e-mailu.

V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?:
- vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a
to z jak?hokoliv d?vodu i bez uveden? d?vodu.
- a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout;
Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce
s dodatkem ?i odchylkou.
- trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m
dosa?en?m shody na v?ech jej?ch n?le?itostech.
- odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost
??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn?
pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn?
osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi
?i osob? j?m zastoupen? zn?m?.

This e-mail and any documents attached to it may be confidential and are
intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender.
Delete the contents of this e-mail with all attachments and its copies from your
system.
If you are not the intended recipient of this e-mail, you are not authorized to
use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by
modifications of the e-mail or by delay with transfer of the email.

In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering into a
contract in any time, for any reason, and without stating any reasoning.
- if the e-mail contains an offer, the recipient is entitled to immediately
accept such offer; The sender of this e-mail (offer) excludes any acceptance of
the offer on the part of the recipient containing any amendment or variation.
- the sender insists on that the respective contract is concluded only upon an
express mutual agreement on all its aspects.
- the sender of this e-mail informs that he/she is not authorized to enter into
any contracts on behalf of the company except for cases in which he/she is
expressly authorized to do so in writing, and such authorization or power of
attorney is submitted to the recipient or the person represented by the
recipient, or the existence of such authorization is known to the recipient of
the person represented by the recipient.

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
>
>
>
>
>

Maybe Matching Threads

Search for more maybe matching threads

R help - Nov 2017 - ggplot inside function doesn't plot

[R] ggplot inside function doesn't plot

[R] ggplot inside function doesn't plot

[R] ggplot inside function doesn't plot

[R] ggplot inside function doesn't plot

Maybe Matching Threads