Re: [R] scaling loess curves
Hi
based on your data maybe using logarithmic y scale shall give you desired
result.
http://stackoverflow.com/questions/4699493/transform-only-one-axis-to-log10-scale-with-ggplot2
Or you can recalculate intensity to scale 100-0 (or any other suitable scale).
?rescale
Cheers
Petr
From: Bogdan Tanasa [mailto:tan...@gmail.com]
Sent: Friday, September 11, 2015 8:14 AM
To: PIKAL Petr; r-help
Subject: Re: [R] scaling loess curves
Hi Petr,
thank you for your reply regarding the scaling of loess curves. Our situation
is the following :
we do have 2 experiments, and for each experiment, the set of data is in the
following format : "nodeA (chr, start, end) - node B (chr, start, end) -
interaction intensity (between A and B)".
We are trying to SCALE the LOESS curves ( for the graphs "distance between node
A and node B" vs "intensity") for experiment1 vs experiment2, in order to make
the experiments directly comparable.
I have attached 2 figures with the LOESS curves for experiment1 and experiment2
to my email. Shall you have any suggestions, please let me know. Thanks a lot,
-- bogdan
On Mon, Sep 7, 2015 at 7:34 AM, PIKAL Petr
<petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> wrote:
Hi
what about xlim or ylim?
Cheers
Petr
> -Original Message-
> From: R-help
> [mailto:r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org>] On
> Behalf Of Bogdan
> Tanasa
> Sent: Monday, September 07, 2015 8:00 AM
> To: r-help
> Subject: [R] scaling loess curves
>
> Dear all,
>
> please could you advise about a method to scale 2 plots of LOESS
> curves.
> More specifically, we do have 2 sets of 5C data, and the loess plots
> reflect the relationship between INTENSITY and DISTANCE (please see the
> R code below).
>
> I am looking for a method/formula to scale these 2 LOESS plots and make
> them directly comparable.
>
> many thanks,
>
> -- bogdan
>
>
>
> -- the R code --
>
>
>
> a <- read.delim("a",header=T)
> qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size =
> 1,
> span=0.01)+xlab("distance")+ylab("intensity")
>
>
>
> b <- read.delim("b",header=T)
> qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size =
> 1,
> span=0.01)+xlab("distance")+ylab("intensity")
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org<mailto:R-help@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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Delete the contents of this e-mail with all attachments and its copies from
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In case that this e-mail forms part of business dealings:
- the se
Re: [R] scaling loess curves
Hi Petr,
thank you for your reply regarding the scaling of loess curves. Our
situation is the following :
we do have 2 experiments, and for each experiment, the set of data is in
the following format : "nodeA (chr, start, end) - node B (chr, start, end)
- interaction intensity (between A and B)".
We are trying to SCALE the LOESS curves ( for the graphs "distance between
node A and node B" vs "intensity") for experiment1 vs experiment2, in order
to make the experiments directly comparable.
I have attached 2 figures with the LOESS curves for experiment1 and
experiment2 to my email. Shall you have any suggestions, please let me
know. Thanks a lot,
-- bogdan
On Mon, Sep 7, 2015 at 7:34 AM, PIKAL Petr <petr.pi...@precheza.cz> wrote:
> Hi
>
> what about xlim or ylim?
>
> Cheers
> Petr
>
>
> > -Original Message-
> > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Bogdan
> > Tanasa
> > Sent: Monday, September 07, 2015 8:00 AM
> > To: r-help
> > Subject: [R] scaling loess curves
> >
> > Dear all,
> >
> > please could you advise about a method to scale 2 plots of LOESS
> > curves.
> > More specifically, we do have 2 sets of 5C data, and the loess plots
> > reflect the relationship between INTENSITY and DISTANCE (please see the
> > R code below).
> >
> > I am looking for a method/formula to scale these 2 LOESS plots and make
> > them directly comparable.
> >
> > many thanks,
> >
> > -- bogdan
> >
> >
> >
> > -- the R code --
> >
> >
> >
> > a <- read.delim("a",header=T)
> > qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size =
> > 1,
> > span=0.01)+xlab("distance")+ylab("intensity")
> >
> >
> >
> > b <- read.delim("b",header=T)
> > qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size =
> > 1,
> > span=0.01)+xlab("distance")+ylab("intensity")
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@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 jakékoliv k němu připojené dokumenty jsou důvěrné a jsou
> určeny pouze jeho adresátům.
> Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě
> neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie
> vymažte ze svého systému.
> Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email
> jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
> Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi
> či zpožděním přenosu e-mailu.
>
> V případě, že je tento e-mail součástí obchodního jednání:
> - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření
> smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu.
> - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout;
> Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany
> příjemce s dodatkem či odchylkou.
> - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve
> výslovným dosažením shody na všech jejích náležitostech.
> - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za
> společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn
> nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto
> emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich
> existence je adresátovi či osobě jím zastoupené známá.
>
> 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 with
Re: [R] scaling loess curves
thanks Petr. It shall work ;)
On Fri, Sep 11, 2015 at 4:34 AM, PIKAL Petr <petr.pi...@precheza.cz> wrote:
> Hi
>
>
>
> you need to merge those two data frames with a column indicating given set.
>
>
>
> Without data it is only a guess but
>
>
>
> a$set<-„a“
>
> b$set<-„b“
>
>
>
> complete <- rbind(a,b)
>
>
>
> p <-ggplot(complete, aes(x=distance, y=intensity, colour=set))
>
> p+geom_smooth(method = "loess", size = 1,
> span=0.01)+xlab("distance")+ylab("intensity")
>
> shall do it.
>
>
>
> Cheers
>
> Petr
>
>
>
> *From:* Bogdan Tanasa [mailto:tan...@gmail.com]
> *Sent:* Friday, September 11, 2015 10:03 AM
>
> *To:* PIKAL Petr; r-help
> *Subject:* Re: [R] scaling loess curves
>
>
>
> Dear Petr,
>
> thank you very much, it helped. On a side note, shall I have 2 plots and 2
> loess curves (as below), is there any way in ggplot2 to overlay these 2
> graphs for "a" and "b" ? much thanks again !
>
> qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size = 1,
> span=0.01)+xlab("distance")+ylab("intensity")
>
> qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size = 1,
> span=0.01)+xlab("distance")+ylab("intensity")
>
> -- bogdan
>
>
>
> On Fri, Sep 11, 2015 at 3:06 AM, PIKAL Petr <petr.pi...@precheza.cz>
> wrote:
>
> Hi
>
>
>
> based on your data maybe using logarithmic y scale shall give you desired
> result.
>
>
>
>
> http://stackoverflow.com/questions/4699493/transform-only-one-axis-to-log10-scale-with-ggplot2
>
>
>
> Or you can recalculate intensity to scale 100-0 (or any other suitable
> scale).
>
>
>
> ?rescale
>
>
>
> Cheers
>
> Petr
>
>
>
> *From:* Bogdan Tanasa [mailto:tan...@gmail.com]
> *Sent:* Friday, September 11, 2015 8:14 AM
> *To:* PIKAL Petr; r-help
> *Subject:* Re: [R] scaling loess curves
>
>
>
> Hi Petr,
>
> thank you for your reply regarding the scaling of loess curves. Our
> situation is the following :
>
> we do have 2 experiments, and for each experiment, the set of data is in
> the following format : "nodeA (chr, start, end) - node B (chr, start, end)
> - interaction intensity (between A and B)".
>
> We are trying to SCALE the LOESS curves ( for the graphs "distance between
> node A and node B" vs "intensity") for experiment1 vs experiment2, in order
> to make the experiments directly comparable.
>
> I have attached 2 figures with the LOESS curves for experiment1 and
> experiment2 to my email. Shall you have any suggestions, please let me
> know. Thanks a lot,
>
>
>
> -- bogdan
>
>
>
> On Mon, Sep 7, 2015 at 7:34 AM, PIKAL Petr <petr.pi...@precheza.cz> wrote:
>
> Hi
>
> what about xlim or ylim?
>
> Cheers
> Petr
>
>
>
> > -Original Message-
> > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Bogdan
> > Tanasa
> > Sent: Monday, September 07, 2015 8:00 AM
> > To: r-help
> > Subject: [R] scaling loess curves
> >
> > Dear all,
> >
> > please could you advise about a method to scale 2 plots of LOESS
> > curves.
> > More specifically, we do have 2 sets of 5C data, and the loess plots
> > reflect the relationship between INTENSITY and DISTANCE (please see the
> > R code below).
> >
> > I am looking for a method/formula to scale these 2 LOESS plots and make
> > them directly comparable.
> >
> > many thanks,
> >
> > -- bogdan
> >
> >
> >
> > -- the R code --
> >
> >
> >
> > a <- read.delim("a",header=T)
> > qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size =
> > 1,
> > span=0.01)+xlab("distance")+ylab("intensity")
> >
> >
> >
> > b <- read.delim("b",header=T)
> > qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size =
> > 1,
> > span=0.01)+xlab("distance")+ylab("intensity")
> >
>
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@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.
>
Re: [R] scaling loess curves
Dear Petr,
thank you very much, it helped. On a side note, shall I have 2 plots and 2
loess curves (as below), is there any way in ggplot2 to overlay these 2
graphs for "a" and "b" ? much thanks again !
qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size = 1,
span=0.01)+xlab("distance")+ylab("intensity")
qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size = 1,
span=0.01)+xlab("distance")+ylab("intensity")
-- bogdan
On Fri, Sep 11, 2015 at 3:06 AM, PIKAL Petr <petr.pi...@precheza.cz> wrote:
> Hi
>
>
>
> based on your data maybe using logarithmic y scale shall give you desired
> result.
>
>
>
>
> http://stackoverflow.com/questions/4699493/transform-only-one-axis-to-log10-scale-with-ggplot2
>
>
>
> Or you can recalculate intensity to scale 100-0 (or any other suitable
> scale).
>
>
>
> ?rescale
>
>
>
> Cheers
>
> Petr
>
>
>
> *From:* Bogdan Tanasa [mailto:tan...@gmail.com]
> *Sent:* Friday, September 11, 2015 8:14 AM
> *To:* PIKAL Petr; r-help
> *Subject:* Re: [R] scaling loess curves
>
>
>
> Hi Petr,
>
> thank you for your reply regarding the scaling of loess curves. Our
> situation is the following :
>
> we do have 2 experiments, and for each experiment, the set of data is in
> the following format : "nodeA (chr, start, end) - node B (chr, start, end)
> - interaction intensity (between A and B)".
>
> We are trying to SCALE the LOESS curves ( for the graphs "distance between
> node A and node B" vs "intensity") for experiment1 vs experiment2, in order
> to make the experiments directly comparable.
>
> I have attached 2 figures with the LOESS curves for experiment1 and
> experiment2 to my email. Shall you have any suggestions, please let me
> know. Thanks a lot,
>
>
>
> -- bogdan
>
>
>
> On Mon, Sep 7, 2015 at 7:34 AM, PIKAL Petr <petr.pi...@precheza.cz> wrote:
>
> Hi
>
> what about xlim or ylim?
>
> Cheers
> Petr
>
>
>
> > -Original Message-
> > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Bogdan
> > Tanasa
> > Sent: Monday, September 07, 2015 8:00 AM
> > To: r-help
> > Subject: [R] scaling loess curves
> >
> > Dear all,
> >
> > please could you advise about a method to scale 2 plots of LOESS
> > curves.
> > More specifically, we do have 2 sets of 5C data, and the loess plots
> > reflect the relationship between INTENSITY and DISTANCE (please see the
> > R code below).
> >
> > I am looking for a method/formula to scale these 2 LOESS plots and make
> > them directly comparable.
> >
> > many thanks,
> >
> > -- bogdan
> >
> >
> >
> > -- the R code --
> >
> >
> >
> > a <- read.delim("a",header=T)
> > qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size =
> > 1,
> > span=0.01)+xlab("distance")+ylab("intensity")
> >
> >
> >
> > b <- read.delim("b",header=T)
> > qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size =
> > 1,
> > span=0.01)+xlab("distance")+ylab("intensity")
> >
>
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@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 jakékoliv k němu připojené dokumenty jsou důvěrné a jsou
> určeny pouze jeho adresátům.
> Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě
> neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie
> vymažte ze svého systému.
> Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email
> jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
> Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi
> či zpožděním přenosu e-mailu.
>
> V případě, že je tento e-mail součástí obchodního jednání:
> - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření
> smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu.
> - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout;
> Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany
> příjemce s do
Re: [R] scaling loess curves
Hi
you need to merge those two data frames with a column indicating given set.
Without data it is only a guess but
a$set<-„a“
b$set<-„b“
complete <- rbind(a,b)
p <-ggplot(complete, aes(x=distance, y=intensity, colour=set))
p+geom_smooth(method = "loess", size = 1,
span=0.01)+xlab("distance")+ylab("intensity")
shall do it.
Cheers
Petr
From: Bogdan Tanasa [mailto:tan...@gmail.com]
Sent: Friday, September 11, 2015 10:03 AM
To: PIKAL Petr; r-help
Subject: Re: [R] scaling loess curves
Dear Petr,
thank you very much, it helped. On a side note, shall I have 2 plots and 2
loess curves (as below), is there any way in ggplot2 to overlay these 2 graphs
for "a" and "b" ? much thanks again !
qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size = 1,
span=0.01)+xlab("distance")+ylab("intensity")
qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size = 1,
span=0.01)+xlab("distance")+ylab("intensity")
-- bogdan
On Fri, Sep 11, 2015 at 3:06 AM, PIKAL Petr
<petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> wrote:
Hi
based on your data maybe using logarithmic y scale shall give you desired
result.
http://stackoverflow.com/questions/4699493/transform-only-one-axis-to-log10-scale-with-ggplot2
Or you can recalculate intensity to scale 100-0 (or any other suitable scale).
?rescale
Cheers
Petr
From: Bogdan Tanasa [mailto:tan...@gmail.com<mailto:tan...@gmail.com>]
Sent: Friday, September 11, 2015 8:14 AM
To: PIKAL Petr; r-help
Subject: Re: [R] scaling loess curves
Hi Petr,
thank you for your reply regarding the scaling of loess curves. Our situation
is the following :
we do have 2 experiments, and for each experiment, the set of data is in the
following format : "nodeA (chr, start, end) - node B (chr, start, end) -
interaction intensity (between A and B)".
We are trying to SCALE the LOESS curves ( for the graphs "distance between node
A and node B" vs "intensity") for experiment1 vs experiment2, in order to make
the experiments directly comparable.
I have attached 2 figures with the LOESS curves for experiment1 and experiment2
to my email. Shall you have any suggestions, please let me know. Thanks a lot,
-- bogdan
On Mon, Sep 7, 2015 at 7:34 AM, PIKAL Petr
<petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> wrote:
Hi
what about xlim or ylim?
Cheers
Petr
> -Original Message-
> From: R-help
> [mailto:r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org>] On
> Behalf Of Bogdan
> Tanasa
> Sent: Monday, September 07, 2015 8:00 AM
> To: r-help
> Subject: [R] scaling loess curves
>
> Dear all,
>
> please could you advise about a method to scale 2 plots of LOESS
> curves.
> More specifically, we do have 2 sets of 5C data, and the loess plots
> reflect the relationship between INTENSITY and DISTANCE (please see the
> R code below).
>
> I am looking for a method/formula to scale these 2 LOESS plots and make
> them directly comparable.
>
> many thanks,
>
> -- bogdan
>
>
>
> -- the R code --
>
>
>
> a <- read.delim("a",header=T)
> qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size =
> 1,
> span=0.01)+xlab("distance")+ylab("intensity")
>
>
>
> b <- read.delim("b",header=T)
> qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size =
> 1,
> span=0.01)+xlab("distance")+ylab("intensity")
>
> [[alternative HTML version deleted]]
>
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[R] scaling loess curves
Dear all,
please could you advise about a method to scale 2 plots of LOESS curves.
More specifically, we do have 2 sets of 5C data, and the loess plots
reflect the relationship between INTENSITY and DISTANCE (please see the R
code below).
I am looking for a method/formula to scale these 2 LOESS plots and make
them directly comparable.
many thanks,
-- bogdan
-- the R code --
a <- read.delim("a",header=T)
qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size = 1,
span=0.01)+xlab("distance")+ylab("intensity")
b <- read.delim("b",header=T)
qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size = 1,
span=0.01)+xlab("distance")+ylab("intensity")
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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] scaling loess curves
Hi
what about xlim or ylim?
Cheers
Petr
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Bogdan
> Tanasa
> Sent: Monday, September 07, 2015 8:00 AM
> To: r-help
> Subject: [R] scaling loess curves
>
> Dear all,
>
> please could you advise about a method to scale 2 plots of LOESS
> curves.
> More specifically, we do have 2 sets of 5C data, and the loess plots
> reflect the relationship between INTENSITY and DISTANCE (please see the
> R code below).
>
> I am looking for a method/formula to scale these 2 LOESS plots and make
> them directly comparable.
>
> many thanks,
>
> -- bogdan
>
>
>
> -- the R code --
>
>
>
> a <- read.delim("a",header=T)
> qplot(data=a,distance,intensity)+geom_smooth(method = "loess", size =
> 1,
> span=0.01)+xlab("distance")+ylab("intensity")
>
>
>
> b <- read.delim("b",header=T)
> qplot(data=b,distance,intensity)+geom_smooth(method = "loess", size =
> 1,
> span=0.01)+xlab("distance")+ylab("intensity")
>
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