Hi,
I was trying as well as looking for an answer without success (a bit strange
since it should be an easy problem) and therefore I will appreciate you
help:
My simple script is:
# Loadings data of 5 columns and 100 rows of data
data1<-read.csv("C:/?/MyPCA.csv")
pairs(data1[,1:4])
pca1 <- princomp(data1[,1:4], score=TRUE, cor=TRUE)
biplot(pca1)
The biplot present the data points as numbers. How can I present the data
point in color (depends on their group-column 5). I was thinking about doing
it using ggplot2 but I can not succeed. Any idea how to do it?
Thanks
--
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It looks like you can if I understand properly. Try this dat1 <- data.frame(dat1$scores) dat1$items <- rownames(data1) ggplot(dat1, aes(Comp.1, Comp.2, colour = items)) + geom_point() + theme(legend.position="none") John Kane Kingston ON Canada> -----Original Message----- > From: ashz at walla.co.il > Sent: Wed, 10 Jul 2013 06:09:00 -0700 (PDT) > To: r-help at r-project.org > Subject: [R] PCA and gglot2 > > Hi, > > I was trying as well as looking for an answer without success (a bit > strange > since it should be an easy problem) and therefore I will appreciate you > help: > > My simple script is: > # Loadings data of 5 columns and 100 rows of data > data1<-read.csv("C:/?/MyPCA.csv") > pairs(data1[,1:4]) > pca1 <- princomp(data1[,1:4], score=TRUE, cor=TRUE) > biplot(pca1) > > The biplot present the data points as numbers. How can I present the data > point in color (depends on their group-column 5). I was thinking about > doing > it using ggplot2 but I can not succeed. Any idea how to do it? > > Thanks > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/PCA-and-gglot2-tp4671225.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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.____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
'Sorry I made a mistake . I was using some data of my own and didn't make some key changes to the script to match your variables. dat1 <- data.frame(pca1 $scores) # creates the data.frame dat1$items <- rownames(data1pca1 ) # adds item names ggplot(dat1, aes(Comp.1, Comp.2, colour = items)) + geom_point() + theme(legend.position="none") A quick look suggests that this is roughly the same plot as in the example Fig 4 but there the author is using geom_segment to add the lines but I have not looked at it all that carefully. John Kane Kingston ON Canada> -----Original Message----- > From: ashz at walla.co.il > Sent: Wed, 10 Jul 2013 11:02:11 -0700 (PDT) > To: r-help at r-project.org > Subject: Re: [R] PCA and gglot2 > > Hi, > > Thanks. Fig 4 in the link you provided is what I am looking for. > > I still do not know how to implement my data1 and pca1 in the script you > provided as I think it is only a part of a full script. > " > data1<-read.csv("C:/?/MyPCA.csv") > pca1 <- princomp(data1[,1:4], score=TRUE, cor=TRUE) > " > > Am I right, how can I implement my data.frames? > > Thanks again > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/PCA-and-gglot2-tp4671225p4671237.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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.____________________________________________________________ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop!
Not sure why the problem. I think I'd need see your actual data and give it a try. If you want to supply your data or a sample of it see ?dput for a convenient way to do so. I see thought that you've found a dedicated ggplot biplot so if may not be worth your while. John Kane Kingston ON Canada> -----Original Message----- > From: ashz at walla.co.il > Sent: Wed, 10 Jul 2013 12:49:55 -0700 (PDT) > To: r-help at r-project.org > Subject: Re: [R] PCA and gglot2 > > Dear John, > > Thanks for the help. > > I did some minor modifications to your script as I had some problems: > ... > pca = PCA(data[,1:4], scale.unit=T, graph=F) > dat1 <- data.frame(pca$scores) # creates the data.frame > dat1$items <- rownames(data$group) # adds item names > ggplot(dat1, aes(pca$ind$coord[,1], pca$ind$coord[,2], colour > dat1$item)) > + geom_point() + theme(legend.position="none") > > I still do not get separation by color by group (column 5 of csv file) as > the dat1 is empty (data frame with 0 columns and 0 rows). > > Any reason why? > > Thanks again. > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/PCA-and-gglot2-tp4671225p4671253.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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.____________________________________________________________ GET FREE SMILEYS FOR YOUR IM & EMAIL - Learn more at http://www.inbox.com/smileys Works with AIM?, MSN? Messenger, Yahoo!? Messenger, ICQ?, Google Talk? and most webmails