Principal Component analysis (PCA) in R

library("ggplot2")
library("gridExtra")
library(ggbiplot)
library("corrplot")
library(factoextra)
#conversion of row number
data=rownames(GGE)=c("Me","E6","E2","E4","KB","HUl","kat","Dan","EA2","Ts",
"E0","E5","DI","E8","E39","ET1","BO","Ab","Si")
pca =prcomp(GGE[,c(2:11)], center = TRUE,scale. = TRUE)
print(pca)
to get eigen value
eig.val = get_eigenvalue(pca)
eig.val
#to get scree plot
fviz_eig(pca, addlabels = TRUE, ylim = c(0, 50))
PCA results for variables
var=get_pca_var(pca)
to see the most contributing variables for each dimension
corrplot(var$cos2, is.corr=FALSE)
#to see the most contributing variables for both dimension
fviz_cos2(pca, choice = "var", axes = 1:2)
to draw a bar plot of variable contributions
Contributions of variables to PC1
a=fviz_contrib(pca, choice = "var", axes = 1)# top= 5 to limit to five var.
Contributions of variables to PC2
b=fviz_contrib(pca, choice = "var", axes = 2)
grid.arrange(a,b, ncol=2, top='Contribution of the variables to the first two PCs')
Total contribution on PC1 and PC2
fviz_contrib(pca, choice = "ind", axes = 1:2)
#Graph of variables
fviz_pca_var(pca,
col.var = "cos2",
gradient.cols = c("red", "blue", "green"),
repel = TRUE)
#Biplot of individuals and variables
fviz_pca_biplot(pca, repel = TRUE,
col.var = "blue",
col.ind = "red")
#########################################################################
#Plotting PCA
ggbiplot(pca)
#This will name each point with the name of the genotypes
ggbiplot(pca,labels=rownames(GGE))
plot using PC1 and PC2
ggbiplot(pca,ellipse=TRUE,choices=c(1,2),labels=rownames(GGE), groups=GGE$ENV)
scale the samples
ggbiplot(pca,ellipse=TRUE,obs.scale = 2, var.scale = 4.5,
labels=rownames(GGE), groups=GGE$ENV)
#remove the arrows altogether
ggbiplot(pca,ellipse=TRUE,obs.scale = 1, var.scale = 1,var.axes=FALSE,
labels=rownames(GGE), groups=GGE$ENV)
final biplot by Customize ggbiplot
aa=ggbiplot(pca,ellipse=TRUE,obs.scale = 1, var.scale = 1, labels=rownames(GGE), groups=GGE$ENV) +
scale_colour_manual(name="Location", values= c("blue", "red", "green","pink"))+
ggtitle("PCA of wakjira")+
theme_minimal()+
theme(legend.position = "bottom")
aa
ggsave(filename = "Waq.png", plot = aa,width = 22, height = 15, dpi = 2500, units = "cm")

[@oromokomacharles1751]

This is by far the best tutorial on doing PCA using R statistics. Thank you so much

[@wakjiratesfahun3682]

Thank you.

[@MengistuGelasso]

The best tutorial on how to compute PCA using R. Thank you!

[@fredericadedopartey3521]

this is by far the best explanatory video on PCA. strangely I can't install corrplot and ggbilot packages

[@wakjiratesfahun3682]

Use this codes
library(devtools)
install_github("vqv/ggbiplot")
########################
devtools::install_github('taiyun/corrplot', build_vignettes = TRUE)
Thanks

[@kantidewi6031]

same here, but it still can't install ggbiplot
@@wakjiratesfahun3682

[@user-qy5uy9fl1p]

thank you so much. This is the best tutorial on running PCA using Rstudio. more grace

[@amadovelasquez6780]

The best explanation that I have found; thank you very much.

[@wakjiratesfahun3682]

Glad it was helpful!

[@johneagle4384]

Thank you. This is a very good explanation of PCA. Very useful, I am using what I learned from it in my research work.

[@wakjiratesfahun3682]

Thank you .

[@birtukantolera4448]

Thank you so much very helpful Waki, Please keep up the good work!.

[@wakjiratesfahun3682]

Thanks burte.

[@simonnjaukariukico-bi2116]

Was very helpful. Thank you Sir.

[@wakjiratesfahun3682]

Thank you for you positive feedback

[@sefawdinberta4515]

Excellent presentation

[@wakjiratesfahun3682]

Thank you so much.

[@nasrmhm]

Thank you for explanations and sharing the helpful and nice work

[@wakjiratesfahun3682]

Thank you brother.

[@JuHP-hy1jo]

Best tutor ever!

[@wakjiratesfahun3682]

Thank you.

[@ManzoorRaieesKhan]

Thanks for uploading this video

[@wakjiratesfahun3682]

I thank you for your suggestion.

[@mohamedlagzouli6679]

well explained
well illustrated

[@wakjiratesfahun3682]

Thank you Mohammed for you constructive feedback.

[@mohamedlagzouli6679]

@@wakjiratesfahun3682 you'r wlcm

[@mailabib3900]

Wonderful video, Thank you very much

[@wakjiratesfahun3682]

Thanks.

[@jimmycliffordoppong7988]

This is really helpful. Thank you. However, do you have transcribed commentaries on what you were saying whilst you were running the codes? it will be helpful since I did not catch some of the things you said.

[@wakjiratesfahun3682]

Sorry I didn't transcribe it.

[@abinashdas3604]

Wonderful video...thank you so much for this 😊

[@wakjiratesfahun3682]

Thank you for your comment.

[@basilotieno2677]

Thank you!!

[@wakjiratesfahun3682]

Thanks

[@abhilashwodeyar]

Wonderful explanation...Thank you so much

[@asradesofi7048]

Thanks for a nice explanation

[@wakjiratesfahun3682]

Thank you.

[@nezifabamecha8037]

Well explained

[@wakjiratesfahun3682]

Thank you brother for your constructive comments.

[@afeezoluniyishittuirri7645]

Thanks Prof for this wonderful lecture. Am having problems installing ggbiplot, any hint you can help me with? thanks

[@wakjiratesfahun3682]

Run this code
library(devtools)
install_github("vqv/ggbiplot")

[@afeezoluniyishittuirri7645]

library(devtools)
Error: package ‘usethis’ 2.1.5 was found, but >= 2.1.6 is required by ‘devtools’
In addition: Warning message:
package ‘devtools’ was built under R version 4.1.3
> install_github("vqv/ggbiplot")
Error in install_github("vqv/ggbiplot") :
could not find function "install_github"= this is the errors I have been having since before I contacted you
@@wakjiratesfahun3682

[@hope2024-g]

Thank you Sir 🙏❤

[@wakjiratesfahun3682]

Thanks bro.

[@saro4761]

Perfect Video thanks

[@wakjiratesfahun3682]

Thanks.

[@WorkuKebedeTekle]

really I like it. Thank you!

[@wakjiratesfahun3682]

Thank you very much.

[@martinazoric4098]

Thank you so much!!! Thank you for sharing knowledge!

[@wakjiratesfahun3682]

Thank you.

[@techalebirhan1399]

The Greatest one !!!!

[@wakjiratesfahun3682]

Thank you.

[@jebelhaji6666]

it is good english
thank you

[@selamawitkebebew3373]

Thanks!

[@wakjiratesfahun3682]

Thank you!

[@saptarshimondal8666]

Awesome tutorial

[@NebiyouMaseboMalore]

Dear, i have tried to search the normality checking youtube that was done by you but I couldn't find it, please would you help me?

[@wakjiratesfahun3682]

I did a tutorial on normality test. Please check my channel.

[@seenaamulatu3825]

Thank you🙏 for your important tutorial. but how do I arrange my data from a simple lattice design? can I use the mean for the parameters??

[@wakjiratesfahun3682]

Yeah you have to use the mean value.

[@NebiyouMaseboMalore]

Too impressive, moreover is there this tube in Amharic language?

[@wakjiratesfahun3682]

Initially planned to give a tutorial in Amharic but due to bunch request , I changed the medium to English.

[@sakisuf3237]

Thanks sir for this video
Sir I want to analyse the effect of physicochemical parameters of waterbody on the distribution of single species of fish.can you please suggest me the appropriate stastical tool .so that I can get results

[@wakjiratesfahun3682]

What is your objective ?

[@gizawwegayehu6103]

Realy nice,

[@wakjiratesfahun3682]

Thanks

[@afeezoluniyishittuirri7645]

Hi Prof please how to fix this error when running this script
fviz_eig(pca, addlabels = TRUE, ylim = c(0, 50))
Error in loadNamespace(j = 3.4.0 is required. I tried to install Cli but still not working. thanks

[@wakjiratesfahun3682]

Uninstall Cli and install the latest package.
Good luck !

[@shittuaoluniyi2535]

OK thanks prof

[@AlemayehuLema]

Thank you

[@wakjiratesfahun3682]

Okay.

[@cengizturkay9230]

I came across this code in PCA analysis.
Error in names(df.v)

[@wakjiratesfahun3682]

Can you share me the code

[@bayisakabe]

If the number of row is large, for example my data has 140 row so what I shall do?

[@pitopizoide]

Thank you for the video! I have a question, for the ggbiplot, how can I select just some variables/axes to represent ?

[@wakjiratesfahun3682]

I didn't get you. Can you elaborate please.

[@subhankarsanyal8138]

superlike

[@wakjiratesfahun3682]

Shukurya Subhankar!

[@Aesthetics10000]

how to label each PC in final chart with traits

[@wakjiratesfahun3682]

Give me the title and I will provide the code for you.

[@cengizturkay9230]

Thanks for video.
I have a question Sir
I can't run the ggbiplot command. I'm trying to download it still doesn't work. How we can solve this problem?
Can you help me

[@wakjiratesfahun3682]

Thanks for the question.

[@wakjiratesfahun3682]

I released a video yesterday . Please check it. You will get answer.

[@cengizturkay9230]

Thanks you Sir
Best

[@cengizturkay9230]

Can we do PCA in a three-factor study ?

[@wakjiratesfahun3682]

@@cengizturkay9230 Pca deals with numbers. Why you bother about factors ?

[@kantidewi6031]

thank you for the explanation, but why i couldn't find this command
(library("ggplot2")
library("gridExtra")
library(ggbiplot)
library("corrplot")
library(factoextra)
it always said error

[@wakjiratesfahun3682]

Can you share the error.

[@GEORONAKUSMAALBARKI]

Sir the ggbiplot is not functin in New Update R ???

[@wakjiratesfahun3682]

what happened?

[@GEORONAKUSMAALBARKI]

@@wakjiratesfahun3682 Have done sir, ggbiplot I get from git hub recently.. and I want ask you about how we can add the colour of contribution line in pca ggbiplot version, like graph Fvis or add some ellipse lshape in graph Fvis.. Thanks

[@nduwayezugilbert7912]

Hi thank you for your video. However, I tried to use your codes with my data but I cannot get the Eigenvalue. I hit this error 'Error in get_eigenvalue(pca) : could not find function "get_eigenvalue".

[@wakjiratesfahun3682]

You forget to run factoextra package .

[@nduwayezugilbert7912]

@@wakjiratesfahun3682 Thank you so much for your assistance. I ran, but I tried to install the "ggbiplot" package in vain; I could not. Any other way to install it?

[@wakjiratesfahun3682]

@@nduwayezugilbert7912 I made a tutorial on some packages that found in other repositories.Please use this code to install ggbiplot.
library(devtools) install_github("vqv/ggbiplot")

[@nduwayezugilbert7912]

@@wakjiratesfahun3682 Thank you so much

[@wakjiratesfahun3682]

@@nduwayezugilbert7912 it's okay.

[@shahadathossen3377]

can I get the data file for practice

[@jebelhaji6666]

Does R software free access?

[@bezawitmekonnen9218]

Well explained

[@wakjiratesfahun3682]

Thank you Beza.

[@user-xu1kv3vq7k]

Sir i changed the rownames but in pca plot it shows same (1,2 ,3....),can you slove this problem pls

[@wakjiratesfahun3682]

your code please