How can I reverse the axis in a biplot
0
When I plot a PCA and then the corresponding biplot, the axis are not always in the same direction, just like in these pictures:
These are the functions, I used:
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
plot(pc$x[,1:2], pch=""); text(pc$x[,1:2], cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
biplot(princomp(dat5, cor=T), cex=.5)
How can I change the axis direction of one of those, to make them the same?
r plot axis pca biplot
asked Nov 21 '18 at 13:54
Nicole Origami Fox
55
add a comment |
0
When I plot a PCA and then the corresponding biplot, the axis are not always in the same direction, just like in these pictures:
These are the functions, I used:
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
plot(pc$x[,1:2], pch=""); text(pc$x[,1:2], cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
biplot(princomp(dat5, cor=T), cex=.5)
How can I change the axis direction of one of those, to make them the same?
r plot axis pca biplot
asked Nov 21 '18 at 13:54
Nicole Origami Fox
55
You second plot is pretty clear, but how did you generate the first one. What ispc?
– G5W
Nov 21 '18 at 14:12
likely the result ofprcomp. A reproducible example always helps by the way
– Vincent Bonhomme
Nov 21 '18 at 14:36
Exactly :) Sorry for beeing too short. This is the prcomp code:
– Nicole Origami Fox
Nov 22 '18 at 18:17
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
– Nicole Origami Fox
Nov 22 '18 at 18:17
Thank you for editing, MrFlick!
– Nicole Origami Fox
Nov 22 '18 at 18:19
add a comment |
0
0
0
When I plot a PCA and then the corresponding biplot, the axis are not always in the same direction, just like in these pictures:
These are the functions, I used:
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
plot(pc$x[,1:2], pch=""); text(pc$x[,1:2], cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
biplot(princomp(dat5, cor=T), cex=.5)
How can I change the axis direction of one of those, to make them the same?
r plot axis pca biplot
asked Nov 21 '18 at 13:54
Nicole Origami Fox
55
When I plot a PCA and then the corresponding biplot, the axis are not always in the same direction, just like in these pictures:
These are the functions, I used:
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
plot(pc$x[,1:2], pch=""); text(pc$x[,1:2], cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
biplot(princomp(dat5, cor=T), cex=.5)
How can I change the axis direction of one of those, to make them the same?
r plot axis pca biplot
r plot axis pca biplot
asked Nov 21 '18 at 13:54
Nicole Origami Fox
55
asked Nov 21 '18 at 13:54
Nicole Origami Fox
55
edited Nov 22 '18 at 18:22
asked Nov 21 '18 at 13:54
Nicole Origami Fox
55
asked Nov 21 '18 at 13:54
Nicole Origami Fox
55
asked Nov 21 '18 at 13:54
Nicole Origami Fox
55
55
You second plot is pretty clear, but how did you generate the first one. What ispc?
– G5W
Nov 21 '18 at 14:12
likely the result ofprcomp. A reproducible example always helps by the way
– Vincent Bonhomme
Nov 21 '18 at 14:36
Exactly :) Sorry for beeing too short. This is the prcomp code:
– Nicole Origami Fox
Nov 22 '18 at 18:17
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
– Nicole Origami Fox
Nov 22 '18 at 18:17
Thank you for editing, MrFlick!
– Nicole Origami Fox
Nov 22 '18 at 18:19
add a comment |
You second plot is pretty clear, but how did you generate the first one. What ispc?
– G5W
Nov 21 '18 at 14:12
likely the result ofprcomp. A reproducible example always helps by the way
– Vincent Bonhomme
Nov 21 '18 at 14:36
Exactly :) Sorry for beeing too short. This is the prcomp code:
– Nicole Origami Fox
Nov 22 '18 at 18:17
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
– Nicole Origami Fox
Nov 22 '18 at 18:17
Thank you for editing, MrFlick!
– Nicole Origami Fox
Nov 22 '18 at 18:19
You second plot is pretty clear, but how did you generate the first one. What is
pc?– G5W
Nov 21 '18 at 14:12
You second plot is pretty clear, but how did you generate the first one. What is
pc?– G5W
Nov 21 '18 at 14:12
likely the result of
prcomp. A reproducible example always helps by the way– Vincent Bonhomme
Nov 21 '18 at 14:36
likely the result of
prcomp. A reproducible example always helps by the way– Vincent Bonhomme
Nov 21 '18 at 14:36
Exactly :) Sorry for beeing too short. This is the prcomp code:
– Nicole Origami Fox
Nov 22 '18 at 18:17
Exactly :) Sorry for beeing too short. This is the prcomp code:
– Nicole Origami Fox
Nov 22 '18 at 18:17
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
– Nicole Origami Fox
Nov 22 '18 at 18:17
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
– Nicole Origami Fox
Nov 22 '18 at 18:17
Thank you for editing, MrFlick!
– Nicole Origami Fox
Nov 22 '18 at 18:19
Thank you for editing, MrFlick!
– Nicole Origami Fox
Nov 22 '18 at 18:19
add a comment |
1 Answer
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The sign of PCs being arbitrary, you can change it/them by multiplying one or more PCs by -1. Note that this stands only for representation only, depending on what you do, eg if you use $rotation you may also need to change the corresponding columns as well. An example with iris follows. Hope this helps.
p <- prcomp(iris[, -5])
plot(p$x[, 1:2], asp=1, xlab="PC1", ylab="PC2")
plot(cbind(p$x[, 1], p$x[, 2]*-1), asp=1, xlab="PC1", ylab="PC2")
answered Nov 21 '18 at 14:33
Vincent Bonhomme
4,41711431
Thank you Vincent! :)
– Nicole Origami Fox
Nov 22 '18 at 18:20
This is how it works for me now:
– Nicole Origami Fox
Nov 22 '18 at 18:35
plot(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2");
– Nicole Origami Fox
Nov 22 '18 at 18:36
text(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2", cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
– Nicole Origami Fox
Nov 22 '18 at 18:37
# I just don't get rid of the symbols with pch="", since I want to use text instead...
– Nicole Origami Fox
Nov 22 '18 at 18:37
|
show 2 more comments
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1 Answer
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votes
1 Answer
1
active
oldest
votes
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oldest
votes
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oldest
votes
2
The sign of PCs being arbitrary, you can change it/them by multiplying one or more PCs by -1. Note that this stands only for representation only, depending on what you do, eg if you use $rotation you may also need to change the corresponding columns as well. An example with iris follows. Hope this helps.
p <- prcomp(iris[, -5])
plot(p$x[, 1:2], asp=1, xlab="PC1", ylab="PC2")
plot(cbind(p$x[, 1], p$x[, 2]*-1), asp=1, xlab="PC1", ylab="PC2")
answered Nov 21 '18 at 14:33
Vincent Bonhomme
4,41711431
Thank you Vincent! :)
– Nicole Origami Fox
Nov 22 '18 at 18:20
This is how it works for me now:
– Nicole Origami Fox
Nov 22 '18 at 18:35
plot(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2");
– Nicole Origami Fox
Nov 22 '18 at 18:36
text(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2", cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
– Nicole Origami Fox
Nov 22 '18 at 18:37
# I just don't get rid of the symbols with pch="", since I want to use text instead...
– Nicole Origami Fox
Nov 22 '18 at 18:37
|
show 2 more comments
2
The sign of PCs being arbitrary, you can change it/them by multiplying one or more PCs by -1. Note that this stands only for representation only, depending on what you do, eg if you use $rotation you may also need to change the corresponding columns as well. An example with iris follows. Hope this helps.
p <- prcomp(iris[, -5])
plot(p$x[, 1:2], asp=1, xlab="PC1", ylab="PC2")
plot(cbind(p$x[, 1], p$x[, 2]*-1), asp=1, xlab="PC1", ylab="PC2")
answered Nov 21 '18 at 14:33
Vincent Bonhomme
4,41711431
Thank you Vincent! :)
– Nicole Origami Fox
Nov 22 '18 at 18:20
This is how it works for me now:
– Nicole Origami Fox
Nov 22 '18 at 18:35
plot(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2");
– Nicole Origami Fox
Nov 22 '18 at 18:36
text(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2", cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
– Nicole Origami Fox
Nov 22 '18 at 18:37
# I just don't get rid of the symbols with pch="", since I want to use text instead...
– Nicole Origami Fox
Nov 22 '18 at 18:37
|
show 2 more comments
2
2
2
The sign of PCs being arbitrary, you can change it/them by multiplying one or more PCs by -1. Note that this stands only for representation only, depending on what you do, eg if you use $rotation you may also need to change the corresponding columns as well. An example with iris follows. Hope this helps.
p <- prcomp(iris[, -5])
plot(p$x[, 1:2], asp=1, xlab="PC1", ylab="PC2")
plot(cbind(p$x[, 1], p$x[, 2]*-1), asp=1, xlab="PC1", ylab="PC2")
answered Nov 21 '18 at 14:33
Vincent Bonhomme
4,41711431
The sign of PCs being arbitrary, you can change it/them by multiplying one or more PCs by -1. Note that this stands only for representation only, depending on what you do, eg if you use $rotation you may also need to change the corresponding columns as well. An example with iris follows. Hope this helps.
p <- prcomp(iris[, -5])
plot(p$x[, 1:2], asp=1, xlab="PC1", ylab="PC2")
plot(cbind(p$x[, 1], p$x[, 2]*-1), asp=1, xlab="PC1", ylab="PC2")
answered Nov 21 '18 at 14:33
Vincent Bonhomme
4,41711431
edited Nov 21 '18 at 17:11
answered Nov 21 '18 at 14:33
Vincent Bonhomme
4,41711431
answered Nov 21 '18 at 14:33
Vincent Bonhomme
4,41711431
answered Nov 21 '18 at 14:33
Vincent Bonhomme
4,41711431
4,41711431
Thank you Vincent! :)
– Nicole Origami Fox
Nov 22 '18 at 18:20
This is how it works for me now:
– Nicole Origami Fox
Nov 22 '18 at 18:35
plot(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2");
– Nicole Origami Fox
Nov 22 '18 at 18:36
text(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2", cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
– Nicole Origami Fox
Nov 22 '18 at 18:37
# I just don't get rid of the symbols with pch="", since I want to use text instead...
– Nicole Origami Fox
Nov 22 '18 at 18:37
|
show 2 more comments
Thank you Vincent! :)
– Nicole Origami Fox
Nov 22 '18 at 18:20
This is how it works for me now:
– Nicole Origami Fox
Nov 22 '18 at 18:35
plot(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2");
– Nicole Origami Fox
Nov 22 '18 at 18:36
text(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2", cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
– Nicole Origami Fox
Nov 22 '18 at 18:37
# I just don't get rid of the symbols with pch="", since I want to use text instead...
– Nicole Origami Fox
Nov 22 '18 at 18:37
Thank you Vincent! :)
– Nicole Origami Fox
Nov 22 '18 at 18:20
Thank you Vincent! :)
– Nicole Origami Fox
Nov 22 '18 at 18:20
This is how it works for me now:
– Nicole Origami Fox
Nov 22 '18 at 18:35
This is how it works for me now:
– Nicole Origami Fox
Nov 22 '18 at 18:35
plot(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2");
– Nicole Origami Fox
Nov 22 '18 at 18:36
plot(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2");
– Nicole Origami Fox
Nov 22 '18 at 18:36
text(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2", cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
– Nicole Origami Fox
Nov 22 '18 at 18:37
text(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2", cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))
– Nicole Origami Fox
Nov 22 '18 at 18:37
# I just don't get rid of the symbols with pch="", since I want to use text instead...
– Nicole Origami Fox
Nov 22 '18 at 18:37
# I just don't get rid of the symbols with pch="", since I want to use text instead...
– Nicole Origami Fox
Nov 22 '18 at 18:37
|
show 2 more comments
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You second plot is pretty clear, but how did you generate the first one. What is
pc?– G5W
Nov 21 '18 at 14:12
likely the result of
prcomp. A reproducible example always helps by the way– Vincent Bonhomme
Nov 21 '18 at 14:36
Exactly :) Sorry for beeing too short. This is the prcomp code:
– Nicole Origami Fox
Nov 22 '18 at 18:17
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
– Nicole Origami Fox
Nov 22 '18 at 18:17
Thank you for editing, MrFlick!
– Nicole Origami Fox
Nov 22 '18 at 18:19