R help - Apr 2019 - Doubt regarding the autoplot function in ggfortify library

Iam using autoplot function from the ggfortify library. I saw that autoplot
gives the 1st two principal components. I am using autoplot to generate 1st
two principal components on a clustered object.
The usage is like :

autoplot(pam(my_data[1:256], 3), label = TRUE, label.size = 4, frame TRUE,
frame.type = 'norm')

So here autoplot generates the principal components on the clustered
object. So can we actually call this a PCA plot? Also what is the algorithm
used by autoplot for generating principal components?

Thanks in advance for the help.



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As I believe the posting guide notes, you may do better addressing
questions about specialized packages to the package maintainers, who often
do not monitor this list.

Cheers,
Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, Apr 25, 2019 at 9:29 AM manju moorthy <manjumoorthy95 at
gmail.com>
wrote:
> Iam using autoplot function from the ggfortify library. I saw that autoplot
> gives the 1st two principal components. I am using autoplot to generate 1st
> two principal components on a clustered object.
> The usage is like :
>
> autoplot(pam(my_data[1:256], 3), label = TRUE, label.size = 4, frame >
TRUE, frame.type = 'norm')
>
> So here autoplot generates the principal components on the clustered
> object. So can we actually call this a PCA plot? Also what is the algorithm
> used by autoplot for generating principal components?
>
> Thanks in advance for the help.
>
>
>
> <
>
http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> >
> Virus-free.
> www.avg.com
> <
>
http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> >
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> 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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True, but reading the supplied help is appropriate before contacting the
maintainer.

Specifically,

help("ggfortify")

and click the link to the index and find the autoplot method in the list and
follow that link.

Or you can read the help for the "pam" function and discover that the
class of the returned object is "pam" so you can use

?autoplot.pam

to go right to it. If the documentation doesn't answer your question you can
communicate that to the maintainer.

You can also just enter

autoplot.pam

at the console and read the source code if it is written in R to see what
calculations are being done.

On April 25, 2019 10:13:30 AM PDT, Bert Gunter <bgunter.4567 at gmail.com>
wrote:
>As I believe the posting guide notes, you may do better addressing
>questions about specialized packages to the package maintainers, who
>often
>do not monitor this list.
>
>Cheers,
>Bert Gunter
>
>"The trouble with having an open mind is that people keep coming along
>and
>sticking things into it."
>-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
>On Thu, Apr 25, 2019 at 9:29 AM manju moorthy
><manjumoorthy95 at gmail.com>
>wrote:
>
>> Iam using autoplot function from the ggfortify library. I saw that
>autoplot
>> gives the 1st two principal components. I am using autoplot to
>generate 1st
>> two principal components on a clustered object.
>> The usage is like :
>>
>> autoplot(pam(my_data[1:256], 3), label = TRUE, label.size = 4, frame
>>> TRUE, frame.type = 'norm')
>>
>> So here autoplot generates the principal components on the clustered
>> object. So can we actually call this a PCA plot? Also what is the
>algorithm
>> used by autoplot for generating principal components?
>>
>> Thanks in advance for the help.
>>
>>
>>
>> <
>>
>http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> >
>> Virus-free.
>> www.avg.com
>> <
>>
>http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> >
>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> 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.
>>
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>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.
-- 
Sent from my phone. Please excuse my brevity.