Skip to content

Instantly share code, notes, and snippets.

@thigm85
Last active March 16, 2021 11:31
Show Gist options
  • Save thigm85/8424654 to your computer and use it in GitHub Desktop.
Save thigm85/8424654 to your computer and use it in GitHub Desktop.
Visualize the difference between PCA and LDA on the iris dataset.
require(MASS)
require(ggplot2)
require(scales)
require(gridExtra)
pca <- prcomp(iris[,-5],
center = TRUE,
scale. = TRUE)
prop.pca = pca$sdev^2/sum(pca$sdev^2)
lda <- lda(Species ~ .,
iris,
prior = c(1,1,1)/3)
prop.lda = r$svd^2/sum(r$svd^2)
plda <- predict(object = lda,
newdata = iris)
dataset = data.frame(species = iris[,"Species"],
pca = pca$x, lda = plda$x)
p1 <- ggplot(dataset) + geom_point(aes(lda.LD1, lda.LD2, colour = species, shape = species), size = 2.5) +
labs(x = paste("LD1 (", percent(prop.lda[1]), ")", sep=""),
y = paste("LD2 (", percent(prop.lda[2]), ")", sep=""))
p2 <- ggplot(dataset) + geom_point(aes(pca.PC1, pca.PC2, colour = species, shape = species), size = 2.5) +
labs(x = paste("PC1 (", percent(prop.pca[1]), ")", sep=""),
y = paste("PC2 (", percent(prop.pca[2]), ")", sep=""))
grid.arrange(p1, p2)
@ivnols
Copy link

ivnols commented Oct 24, 2016

Hi,
I have a question.

My data.frame have a colum with species names (the first colum) and I want to insert these names in each point. Is it possible?

@kelsimarie7
Copy link

kelsimarie7 commented Mar 11, 2018

yes, you can simply add "labels = yourcolumname"
at least this will work for ggbiplot()

@Vikas-Bhaneriya
Copy link

there is some fault here in line 12

it should be 'r' in place of 'lda' on left side

> lda <- lda(Species ~ ., 
>            iris, 
>            prior = c(1,1,1)/3)
> 

should be like


> 
> r <- lda(Species ~ ., 
>            iris, 
>            prior = c(1,1,1)/3)
> 

@BayramSarilmaz
Copy link

BayramSarilmaz commented Jul 29, 2018

Dear @thigm85 ,
I'm getting this error (Error in UseMethod("predict") :
no applicable method for 'predict' applied to an object of class "function") when running

plda <- predict(object = lda,
                newdata = iris)

Any idea how to fix this?

@kindofausername
Copy link

Works fine for me.
Did you load the package correctly?

Dear @thigm85 ,
I'm getting this error (Error in UseMethod("predict") :
no applicable method for 'predict' applied to an object of class "function") when running

plda <- predict(object = lda,
                newdata = iris)

Any idea how to fix this?

@NIOZ-QingZ
Copy link

Hi, it's a cool code to visualize the PCA and LDA.
But I wonder whether you also have an approach to add the arrows of different discriminators onto the LDA plot, so that the contribution and relationship of these discriminators can be partly read simultaneously.
KR - Qing

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment