[R] How to plot PCA output?

[Christian Cole]

Hi Jessica,


THanks for pointing that out. The scaling in biplot() doesn't seem to make
sense to me, however. The default value for scale=1 therefore lambda ^
(1-scale) -> lambda ^ 0 which is 1 regardless of what lambda is. Which
can't be right?

Anyway, I won't worry about it anymore as you and Bryan have confirmed
that I am doing the right thing by plotting the $x data and will ignore
biplot().

Many thanks,

Chris

On 07/05/2012 15:25, "Jessica Streicher" <j.streicher at micromata.de> wrote:

>And i always forget the question..
>
>I haven't understood biplots a 100%, but from what i gleaned this scaling
>is done so it looks better/is easier to read, while the scaling retains
>certain properties of the biplot (something about projecting).
>
>If you want to use the data for anything else, i wouldn't use that
>scaling, just use what the prcomp() or princomp() function returns to you.
>
>
>Am 07.05.2012 um 16:11 schrieb Jessica Streicher:
>
>> Biplot, depending on what parameters you give it, scales the data in a
>>certain way.
>>
>> See
>>http://stat.ethz.ch/R-manual/R-patched/library/stats/html/biplot.princomp
>>.html
>>
>> scale
>> The variables are scaled by lambda ^ scale and the observations are
>>scaled by lambda ^ (1-scale) where lambda are the singular values as
>>computed by princomp. Normally 0 <= scale <= 1, and a warning will be
>>issued if the specified scale is outside this range.
>>
>>
>>
>> Am 07.05.2012 um 16:01 schrieb Christian Cole:
>>
>>> Hi Jessica,
>>>
>>> Yes, that does help. It confirms my digging around in the prcomp
>>>object.
>>>
>>> I was plotting $x, but wasn't sure whether this was appropriate. Mainly
>>> because the data ranges are different in $x than when plotted by
>>>biplot()
>>> - as I mentioned my reply to Bryan. Do you know if this difference is
>>>data
>>> range matters?
>>> Many thanks,
>>>
>>> Chris
>>>
>>>
>>>
>>> On 07/05/2012 14:24, "Jessica Streicher" <j.streicher at micromata.de>
>>>wrote:
>>>
>>>> That depends on what you want to plot there. Basically, you could just
>>>> use plot() with pcaResult$x. You might need to define which PCs you
>>>>want
>>>> to plot there though.
>>>>
>>>> pcaResult<-prcomp(iris[,1:4])
>>>> plot(pcaResult$x) # gives the first 2 PCs
>>>> plot(pcaResult$x[,2:3]) #gives the second vs the 3rd PC
>>>>
>>>> or if you want to see more you can use pairs()
>>>>
>>>> pairs(pcaResult$x)
>>>>
>>>> if you want things colored, theres the col parameter that works for
>>>>both
>>>> functions:
>>>>
>>>> pairs(pcaResult$x,col=iris[,5])
>>>>
>>>> Does this help?
>>>>
>>>> Am 07.05.2012 um 12:22 schrieb Christian Cole:
>>>>
>>>>> I have a decent sized matrix (36 x 11,000) that I have preformed a
>>>>>PCA
>>>>> on
>>>>> with prcomp(), but due to the large number of variables I can't plot
>>>>>the
>>>>> result with biplot(). How else can I plot the PCA output?
>>>>>
>>>>> I tried posting this before, but got no responses so I'm trying
>>>>>again.
>>>>> Surely this is a common problem, but  I can't find a solution with
>>>>> google?
>>>>>
>>>>>
>>>>> The University of Dundee is a registered Scottish Charity, No:
>>>>>SC015096
>>>>>
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list
>>>>> 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.
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> 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.
>>>>
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>
>>
>>
>>      [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> 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.
>
>______________________________________________
>R-help at r-project.org mailing list
>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.
>


The University of Dundee is a registered Scottish Charity, No: SC015096