Worked Example: PCA on SNPs data from a vcf file Part 2 - Data Analysis
2022-11-23
Introduction
The example is split into 2 Parts:
- Part 1: Data Preparation
- Part 2: Data analysis with PCA (this file)
Part 1 must be completed first to create a file,
SNPs_cleaned.csv, that has been completely prepared for
analysis.
Now in Part 2, you will analyze the data with PCA. The steps here will be:
- Center the data (
scale()) - Run a PCA analysis (
prcomp()) - Evaluate the scree plot from the PCA
(
screeplot()) - Evaluate the amount of variation explained by the first 2 PCs.
- Extract the PCA scores for plotting
(
vegan::scores()) - Plot the data
Tasks
In the code below all code is provided. Your tasks will be to do 4 things:
- Give a meaningful title to all sections marked “TODO: TITLE”
- Write 1 to 2 sentences describing what is being done and why in all sections marked “TODO: EXPLAIN”
- Add titles and axes to plots in all sections marked “TODO: UPDATE PLOT”
- Write 1 or 2 sentences interpreting the output from R in all sections marked “TODO: INTERPRET”
Preliminaries
Load the vcfR package with library()
library(vcfR) # KEY## Warning: package 'vcfR' was built under R version 4.2.2##
## ***** *** vcfR *** *****
## This is vcfR 1.13.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
## ***** ***** ***** *****library(vegan)## Warning: package 'vegan' was built under R version 4.2.2## Loading required package: permute## Warning: package 'permute' was built under R version 4.2.2## Loading required package: lattice## This is vegan 2.6-4library(ggplot2)
library(ggpubr)Set the working directory
setwd("C://Users/Grief Mage/Documents")Load the data
SNPs_cleaned <- read.csv(file = "SNPs_cleaned.csv")
warning("If this didn't work, its may be because you didn't set your working directory.")## Warning: If this didn't work, its may be because you didn't set your working
## directory.Data analysis
Scaling the data
Before we can analyze the data with PCA, it is very important to scale the data. This is because we are using data that could vary highly which could affect the visual results. Scaling data doesn’t change the relationships between the numbers but makes the visual output more desirable.
SNPs_scaled <- scale(SNPs_cleaned)Run the PCA
After the PCA is scaled, we can run the PCA using the “prcomp” function. The result is of type “prcomp”.
pca_scaled <- prcomp(SNPs_scaled)Evaluating Relative Importance of PCs
The screeplot shows the relative importance of each PC which is good for seeing how many PCs we should take into account. This done by using the scaled data to get a desirable result.
screeplot(pca_scaled,
ylab = "Relative importance",
main = "Relative importance of PCs Plot")
Based on the screeplot, it is clear that only PC1 has importance to this PCA. This is true because the drop of importance from PC1 to PC2 is dramatic as well as the fact that PC2 through PC10 is about the same level of relative importance.
Percent variation of PCs
Using the summary of the scaled PCA data, we can visualize the variation of the PCs with a barplot
summary_out_scaled <- summary(pca_scaled)PCA_variation <- function(pca_summary, PCs = 2){
var_explained <- pca_summary$importance[2,1:PCs]*100
var_explained <- round(var_explained,1)
return(var_explained)
}var_out <- PCA_variation(summary_out_scaled,PCs = 10)N_columns <- ncol(SNPs_scaled)
barplot(var_out,
main = "Percent variation Scree plot",
ylab = "Percent variation explained")
abline(h = 1/N_columns*100, col = 2, lwd = 2)
The graph shows that the percent variation is fairly evenly spread after PC1. Despite is seeming like PC1 carries most of the variation, it’s only about 20%-25% of the total variation. Typically I would go to around four or five PCs to reduce varibility, but in this case we could go to PC10 to get our desired variability. For the sake of not considering too many variables I will go to the second PC
Incorrect display of PC relationships
Running the “biplot()” on the scaled PCA data provides us with the relationship between PC1 and PC2 in the biplot. The biplot also shows the relationship of samples in each PC as well as the relationship of all PCs with PC1 and PC2.
biplot(pca_scaled)
This is a bad idea because although it does display valuable information, the relationship between PC1-2 and PC3-68 is not needed as we are only going to PC2. On top of that, the data is clearly not very readible.
Extracting PCA scores
The PCA scores get extracted using the “vegan::scores()” on the scaled PCA data. This data provides us the information on on the relationships of PCs with each other as well as
pca_scores <- vegan::scores(pca_scaled)
pca_scores## PC1 PC2 PC3 PC4 PC5
## site1 -16.150981 4.78277919 -4.54818998 6.9690646 -11.397194401
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## PC6 PC7 PC8 PC9 PC10
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## site59 -0.61330079 -0.63267413 -0.89839293 4.897223e-02 3.39326625
## site60 -0.61415036 0.17999878 1.58931814 1.879232e-01 0.64926676
## site61 3.00958941 -2.79857001 -4.11398520 9.856250e-02 2.64891617
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## site65 -0.75769578 -1.91690797 -1.66266037 2.211305e+00 1.81777117
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## site68 1.82940616 -1.98514898 1.16219556 -1.134689e+00 -4.21562017
## PC16 PC17 PC18 PC19 PC20
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## site2 -3.95033161 -4.3305852 5.32434748 2.13813150 -3.2711524
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## site5 4.63405927 0.9764541 9.08934723 5.73999640 4.5498304
## site6 3.87925100 11.7307680 -2.36272993 -5.77947224 8.5404104
## site7 -2.97511211 0.7655208 -2.45883635 1.84982746 5.0753529
## site8 -2.46164556 1.2840060 0.02507114 3.57737461 -0.3886867
## site9 0.53717459 -8.7277219 11.41666212 3.09297530 -7.3377755
## site10 -1.44973703 -4.1816204 -4.77540982 2.27698921 14.0710938
## site11 2.12994849 -3.7348783 -2.61212113 1.15571677 -11.0211937
## site12 0.92659801 -2.2960943 -0.83792567 0.21511899 4.1928080
## site13 -7.43602366 -12.3178185 -5.89946418 -16.41778537 -12.0393690
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## site17 2.54595681 8.6019140 2.59105248 2.22452790 -0.4401765
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## site19 2.46475148 2.0536009 -0.14978910 7.70776887 -3.5290033
## site20 4.07128919 13.8675329 -5.18332533 2.63727603 4.0766910
## site21 0.64082224 1.8806171 -4.54196541 8.71820090 -8.2340354
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## site45 2.18785633 -0.7557845 -1.13727004 0.25371443 -0.5038393
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## site51 -5.48664188 -1.2824532 7.17737614 1.96170211 6.0741685
## site52 1.41817117 -0.5849291 -0.08995004 0.57230490 -0.8697136
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## site54 -2.14672243 4.6504410 -4.20224024 -2.76877374 -1.5181930
## site55 -1.14942902 0.3397144 3.97188461 1.30819522 -3.8273156
## site56 -7.64516378 1.9812179 2.21416393 -0.15403886 -0.2842939
## site57 4.21764388 -0.1591294 -4.03895128 -0.24918824 -1.2591699
## site58 10.55080372 -5.8125053 -4.21861451 0.50654822 2.4662757
## site59 3.22217701 -3.0364319 -0.40937618 1.09860596 1.8909976
## site60 2.34123332 -1.6346622 0.83248157 0.91541552 0.3468963
## site61 -6.76755184 9.0586710 -8.05809776 -8.94999547 -0.8376222
## site62 -4.55836918 2.3479429 3.61384676 2.00370240 0.4017670
## site63 -1.58591917 -0.7454692 6.29217912 4.25992205 1.5341148
## site64 1.45775117 -1.3227433 1.33544784 2.16682482 -0.8307231
## site65 3.40624787 -1.1640304 -3.76016717 -0.21955093 0.3578465
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## site68 -1.13846247 1.7466180 -0.75503144 -1.53544367 -1.3351355
## PC21 PC22 PC23 PC24 PC25
## site1 1.52127677 2.565231e+00 2.84867213 -14.51133159 0.61703924
## site2 1.18958045 -2.353871e+00 4.40090903 4.95007638 5.94616020
## site3 6.76569437 -4.099389e+00 -6.54327475 -1.32628232 -4.63202178
## site4 -0.16432096 -3.789688e+00 -1.78292097 9.65744698 7.42835675
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## site8 -1.67380508 -1.772087e+00 1.16230894 2.19537365 4.56303504
## site9 5.17608303 -7.201598e-01 9.96894365 2.00565517 6.17165527
## site10 -4.01785476 -3.918991e+00 4.06441196 -4.76660074 5.45954772
## site11 8.43616499 -3.644659e-01 3.46244451 4.70352924 0.50464610
## site12 -4.61472983 9.260979e+00 -6.98693271 7.12665522 -4.32921515
## site13 -9.43539663 1.280679e+00 -3.59278229 -5.20667811 -9.60392700
## site14 11.40782375 8.081263e-01 -2.49512852 -0.81742923 -4.02346980
## site15 -5.49645630 1.220836e+01 -4.53821114 11.95704813 -8.28725793
## site16 -4.10755195 2.860850e+00 -0.03938179 3.10323219 7.23386316
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## site18 -4.27727825 -4.327283e+00 -1.54646339 2.90074496 3.29903897
## site19 -7.17847126 9.337153e-01 2.37105845 0.52888429 0.91682211
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## site22 10.69652187 -1.306515e+01 2.05694067 9.01323207 -3.72775680
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## site24 -1.00089445 1.468159e+00 -0.01020607 -0.34639456 1.94984859
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## site37 1.61795852 6.212046e-01 0.05403457 1.72428369 0.75208712
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## site54 0.58936799 2.142771e+00 7.19036001 1.65080290 0.46224481
## site55 -1.36007963 3.094382e+00 2.16021895 -2.02765810 0.03343736
## site56 0.96323542 -2.520177e+00 -7.18348633 -1.36642467 0.69877885
## site57 0.91455946 -2.226518e+00 3.98402166 1.85056632 -3.96681927
## site58 -0.57516854 8.398843e-01 4.41692100 0.67361231 -0.73542564
## site59 -0.61550767 -1.364672e+00 -0.99928936 -0.69065494 -0.20479610
## site60 -0.17161856 -9.302272e-01 -0.66618845 0.42919489 -0.51671493
## site61 6.01158593 1.116473e+01 10.19468613 5.70947556 -1.88231165
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## site68 0.80968484 1.642903e+00 1.81935236 0.66659776 -0.21505206
## PC26 PC27 PC28 PC29 PC30
## site1 1.74232008 1.93760232 3.06699931 -4.012591148 -0.29814505
## site2 -2.92706227 -0.23479646 -3.02277877 -0.454970690 0.93670158
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## site4 12.66292707 -4.26533153 -9.09091694 1.368026318 6.00986306
## site5 -0.99916623 2.89999959 -7.35460672 -2.182545834 9.75191227
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## site8 -2.98349356 -1.53223508 -2.87011402 4.123740483 1.62042332
## site9 -10.42055418 1.67768962 -5.88741326 6.608253134 -6.67748094
## site10 -3.23657815 -1.97996733 -0.34802238 -1.914463716 -5.34042570
## site11 5.96029905 0.89676472 1.73104060 -2.192368816 2.93215082
## site12 0.49643391 -2.27416917 -1.96938361 3.421484512 -4.88325086
## site13 0.82967506 0.58635148 -2.77695075 -1.641563844 0.44653127
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## site17 -10.21263047 3.81764369 9.01991783 -1.060992212 3.72527247
## site18 5.57557618 -0.47015762 3.94720291 1.708237787 3.91015720
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## site52 1.04953661 -5.69949676 0.76535318 -1.553210588 -2.18953382
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## site55 4.42977975 -0.41611673 1.62504662 -0.904316630 -2.02117937
## site56 -4.21606619 -3.63389881 -1.29289019 -0.004557999 2.01248072
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## site58 7.30045761 -7.90581708 5.11481961 3.393527995 4.82048491
## site59 0.23781093 -1.09399267 2.09911834 3.315402674 0.31463238
## site60 0.05120753 -0.22251119 1.10348931 -0.006402868 -1.00773319
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## site68 -1.29487162 1.22373410 -0.77642389 0.104617084 0.38637464
## PC31 PC32 PC33 PC34 PC35
## site1 -0.8449786 -1.260638e-01 -3.61377530 4.10256453 4.23979233
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## site5 6.5845556 4.272106e+00 9.85530300 -3.31718889 -14.20571808
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## site7 0.1012276 2.483815e+00 0.78436479 3.11427077 -2.17581364
## site8 1.5319026 5.844086e-01 1.30899041 -0.02750696 -2.35271916
## site9 -7.4553627 -3.811712e+00 -4.08320295 5.88347757 1.46615977
## site10 -4.2391974 -1.929039e+00 -1.80494873 3.35627821 2.09181204
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## site56 1.231304778 0.93386651 -0.678334593 0.193441588 1.253838365
## site57 -1.889671636 0.15400513 -0.917752506 0.379389809 -0.658977212
## site58 -1.225942445 -0.45614089 0.136780390 -0.673878649 0.723226887
## site59 0.377286071 0.38168629 0.139708148 -0.895726885 -1.101824921
## site60 11.218402336 3.53389950 -2.363458139 1.960883586 1.262444081
## site61 0.140215098 0.45827265 0.422763010 0.060575088 -0.165582809
## site62 -0.594378722 -0.62107277 0.206793012 -0.255972906 1.395303236
## site63 0.278943158 0.31091884 0.117976809 -0.000383430 0.922427116
## site64 -1.361968658 -0.26290135 -2.279053868 -1.914227031 -1.759624090
## site65 1.159239945 0.91983687 -0.865871696 0.286387862 -1.973457053
## site66 2.985271556 1.02758601 0.336730249 1.010887033 -0.114548818
## site67 -1.182966449 -0.41688257 -0.872646389 -0.728608197 -0.670170726
## site68 -0.729003002 -0.32989353 -0.857546580 -0.072577108 0.597169646
## PC66 PC67 PC68
## site1 0.25887920 -0.071769164 3.892704e-15
## site2 0.12454320 0.105779378 5.526341e-14
## site3 -0.07633258 -0.398583275 5.243886e-15
## site4 -0.11887366 -0.110486552 -1.191202e-14
## site5 0.14307481 0.111953379 3.567405e-14
## site6 -0.05460709 -0.280228888 1.748930e-14
## site7 0.14070545 -0.009829872 3.880435e-14
## site8 -0.28486535 0.046058915 -9.299202e-16
## site9 -0.33603898 0.142422536 6.479185e-15
## site10 -0.30725024 -0.171880869 -2.168946e-15
## site11 -0.15993648 -0.065006735 1.228509e-15
## site12 0.26466599 0.011931880 -1.588681e-15
## site13 0.20906731 0.159979058 -4.903738e-15
## site14 -0.35471265 0.072669611 2.598507e-15
## site15 -0.52384743 0.234050681 2.584506e-15
## site16 0.23303718 -0.330701310 1.701644e-14
## site17 0.08964182 0.124711895 -7.384393e-15
## site18 -0.25471205 0.001137405 1.491405e-14
## site19 -0.01173648 0.259513254 -8.171957e-15
## site20 -0.17733310 0.101960367 -1.365282e-14
## site21 0.24572907 0.088676997 -2.194100e-15
## site22 -0.37554830 -0.180851922 -1.381023e-15
## site23 0.04078429 -0.056599579 6.625544e-15
## site24 -0.19577801 0.123900328 -6.711320e-15
## site25 -0.23297624 0.050166076 1.793521e-15
## site26 -0.02186814 -0.258533612 1.608616e-15
## site27 0.01552896 0.192151439 8.280160e-15
## site28 0.16603277 -0.171118298 -3.667437e-15
## site29 -0.44577941 0.244581121 -6.269291e-15
## site30 -0.18915249 -0.140358994 -6.751652e-15
## site31 -0.17315281 0.436750373 -7.379188e-15
## site32 -0.56424465 0.024196753 -2.902858e-15
## site33 0.66614739 -0.446664222 -2.941022e-15
## site34 0.23730471 -0.192871957 -2.847223e-15
## site35 -7.32245000 1.549152880 -1.166049e-14
## site36 0.37056289 -0.843782712 -3.807393e-15
## site37 14.45098047 -4.535399839 -7.684933e-15
## site38 0.09154836 -0.492126926 4.334975e-16
## site39 -0.00175165 0.343053508 -4.299310e-15
## site40 -3.46059710 0.806501265 -9.001155e-15
## site41 -1.89944043 0.853980998 -1.039154e-14
## site42 5.10164319 15.289799775 -6.909078e-15
## site43 -0.09422860 0.371879861 2.143576e-15
## site44 -0.01493225 0.319309375 1.340106e-14
## site45 -0.07908277 -0.102701236 -8.936103e-15
## site46 -2.04799715 -0.678620421 -7.363266e-15
## site47 0.92650612 -2.167954050 -8.131191e-15
## site48 0.04022664 -0.438351197 -1.670213e-15
## site49 -0.68839872 -1.788985019 -8.169045e-15
## site50 -1.12103605 -2.293986149 -1.578014e-14
## site51 -0.06722644 -0.407967986 4.361419e-14
## site52 -0.54592453 -0.364293408 -1.013306e-14
## site53 0.03159422 0.633428480 2.980038e-15
## site54 -0.48673017 -1.418488567 -4.339086e-15
## site55 0.17039794 -0.395649464 -2.323337e-15
## site56 0.19451684 0.429825683 -1.466120e-14
## site57 -0.21459565 -0.513876793 -6.884792e-15
## site58 -0.05539652 -0.088642855 -1.229626e-14
## site59 -0.45210950 -0.484867380 -2.367482e-14
## site60 0.21320444 -1.082987012 3.104056e-15
## site61 -0.42298422 -0.722907101 -9.144270e-15
## site62 -0.06754894 -0.961661365 -4.450616e-15
## site63 0.24078070 0.147297218 -1.414288e-14
## site64 -0.53609221 -0.011562358 -3.630141e-15
## site65 0.18152187 -1.138407140 -4.290188e-16
## site66 0.13094847 0.095265785 -1.003214e-14
## site67 -0.48154695 0.279380015 -8.675894e-15
## site68 -0.06075828 0.167237939 1.169540e-14This is a way of organizing the samples into distinct, seperable groups using the population ID assigned to them from the start.
pop_id <- c("Nel","Nel","Nel","Nel","Nel","Nel","Nel","Nel",
"Nel", "Nel", "Nel", "Nel", "Nel", "Nel", "Nel", "Alt",
"Alt", "Alt", "Alt", "Alt", "Alt", "Alt", "Alt", "Alt",
"Alt", "Alt", "Alt", "Alt", "Alt", "Alt", "Sub", "Sub",
"Sub", "Sub", "Sub", "Sub", "Sub", "Sub", "Sub", "Sub",
"Sub", "Cau", "Cau", "Cau", "Cau", "Cau", "Cau", "Cau",
"Cau", "Cau", "Cau", "Cau", "Cau", "Div", "Div", "Div",
"Div", "Div", "Div", "Div", "Div", "Div", "Div", "Div",
"Div", "Div", "Div", "Div")The variable “pca_scores2” is being turned into a data frame using the function “data.frame()” and it includes the population IDs as well as the numeric values useful for evaluating the data.
pca_scores2 <- data.frame(pop_id,
pca_scores)
pca_scores2## pop_id PC1 PC2 PC3 PC4 PC5
## site1 Nel -16.150981 4.78277919 -4.54818998 6.9690646 -11.397194401
## site2 Nel -14.586377 5.20263466 13.34032366 10.5641951 -16.373975630
## site3 Nel -14.288178 10.78706697 -5.42702396 4.0726079 -2.623913662
## site4 Nel -14.351803 2.79898388 1.10873450 -1.5760956 0.372135269
## site5 Nel -14.201010 -4.68715095 2.02295689 3.5193810 -2.001882146
## site6 Nel -14.505163 4.07600999 11.81730623 7.9658909 -9.620130833
## site7 Nel -14.731929 12.83700675 23.20039945 -10.6930224 7.225229643
## site8 Nel -14.569985 10.88400493 -23.14690961 16.6876939 -2.158970665
## site9 Nel -14.061563 -3.74604898 3.67715489 -1.9948343 3.021100821
## site10 Nel -15.085379 4.72592577 -6.54204045 1.8756569 -0.768521598
## site11 Nel -14.371169 10.30187192 6.46553160 -1.0892358 -1.627716551
## site12 Nel -13.636814 3.40387056 0.21810156 0.8085282 -1.162287141
## site13 Nel -13.833436 -4.31079924 5.09777653 5.0961041 -1.573544952
## site14 Nel -14.094085 1.13655569 0.41703234 6.1310320 -6.054295334
## site15 Nel -14.022729 2.25541648 -3.08228779 2.6167180 -4.867985387
## site16 Alt -13.793931 1.76699466 -1.15622998 -4.4670206 2.282538620
## site17 Alt -12.438187 1.04549411 3.25597275 -0.9184292 2.982358483
## site18 Alt -14.253564 0.85511840 -3.95687473 -3.1898515 1.835438147
## site19 Alt -13.507484 3.59447996 -0.86812443 -4.9887973 6.604962798
## site20 Alt -13.657114 -1.18729090 4.90487853 -1.1145863 -0.479025699
## site21 Alt -13.887411 2.85934874 -2.79313796 -4.1633500 5.442006161
## site22 Alt -14.836926 4.26978525 -4.14451645 -6.3026526 6.850506040
## site23 Alt -15.599265 9.15981345 -1.41703268 -0.4841424 1.929172009
## site24 Alt -13.614478 1.13993944 -1.35374131 -1.8835599 1.905547883
## site25 Alt -14.817293 5.10406589 -0.27597894 -3.3866123 4.738864825
## site26 Alt -14.091995 1.94911864 -2.52888438 -3.3177951 3.717688193
## site27 Alt -14.754507 -0.56268484 -0.90088471 -1.9075044 4.924910218
## site28 Alt -14.000070 4.25655659 -4.03551633 -5.9439556 4.675040375
## site29 Alt -13.676813 0.80458090 0.45453981 -3.5311183 2.436287742
## site30 Alt -14.589789 -2.30170407 -5.77147694 -9.2902832 4.092274641
## site31 Sub -4.775861 -5.92042584 1.17849770 -0.3688342 0.611824826
## site32 Sub -9.063638 -11.06854106 -0.55043006 0.3088628 1.105752536
## site33 Sub -13.199136 -8.95613365 -3.77395469 -0.3650004 -1.952503377
## site34 Sub -13.563343 -12.45669347 -3.07695410 -0.1050671 -0.704921994
## site35 Sub -6.908009 -9.79067122 0.92258566 1.3312917 -1.363306716
## site36 Sub -7.793303 -6.12393039 1.14724572 -0.2404258 -0.624706822
## site37 Sub -5.785882 -7.09849927 0.65790028 1.1949896 -0.541654543
## site38 Sub -13.432413 -11.63530504 -3.49533166 -2.1154883 -1.716288883
## site39 Sub -11.761861 -16.34501103 0.20254467 -0.2102117 0.003899825
## site40 Sub -6.691440 -6.18044176 1.06660867 0.5697113 0.069632134
## site41 Sub -9.064977 -10.98770946 2.12295581 1.7479463 -1.048168324
## site42 Cau 13.037437 0.16626743 -0.84613375 0.6806291 1.151654737
## site43 Cau 21.121955 -1.26978391 10.27655087 11.0890542 -2.249934758
## site44 Cau 22.470742 -1.03154926 0.19792791 -0.7171380 1.169286639
## site45 Cau 20.933057 -0.36442755 0.13036034 -0.8873581 -0.902948174
## site46 Cau 16.156596 0.07614883 0.66065785 -0.3162481 -0.891917167
## site47 Cau 14.680630 0.45811362 0.47701041 1.1755532 0.642358155
## site48 Cau 22.573574 1.12185262 0.03525679 1.9036637 3.582915118
## site49 Cau 12.779425 -1.12552793 2.29692740 2.3080366 1.754324807
## site50 Cau 18.503292 0.16105140 1.26972535 3.1410737 1.673517272
## site51 Cau 21.071272 -0.68652313 0.10792838 0.7551170 0.710535426
## site52 Cau 17.478275 -0.44046797 0.48664126 1.2676555 1.824902055
## site53 Cau 21.551387 0.64167449 -0.11098141 -0.8580289 -1.904469526
## site54 Div 20.430449 2.30144393 -3.00435593 -1.3253268 1.205935652
## site55 Div 22.404670 5.57517881 -1.08754440 2.1779433 5.672129841
## site56 Div 22.108499 1.33625478 0.13396851 2.8535146 2.336687234
## site57 Div 17.168163 -1.76640307 0.26090316 0.7072794 1.847415191
## site58 Div 21.543068 -1.26004502 0.74939849 0.1015705 1.859076030
## site59 Div 21.674688 -0.15705704 1.50489987 2.5150360 2.231165985
## site60 Div 18.692008 0.14561357 1.14910739 2.1347897 1.908605951
## site61 Div 22.647853 3.25455985 -4.15559486 2.1891217 5.021087175
## site62 Div 20.694085 -1.00780227 -1.47002314 -4.1306742 -3.958104647
## site63 Div 21.607826 -0.16866873 0.54644914 -1.0234931 -0.394520790
## site64 Div 16.950330 2.20026505 0.65777853 1.3165483 2.797623456
## site65 Div 19.741046 0.87654736 -2.94823300 -2.7051169 -1.552719651
## site66 Div 18.852479 -0.88383547 0.63759591 2.5942162 1.909374916
## site67 Div 20.523340 2.00427453 -2.03776950 0.2822848 1.995358734
## site68 Div 22.653148 3.20446341 -6.35197764 -25.0415031 -27.605516189
## PC6 PC7 PC8 PC9 PC10
## site1 3.584505683 -1.20694342 4.72730360 -9.09131774 20.44090268
## site2 12.456658264 8.08326046 -1.05691922 -6.55457046 -16.91304525
## site3 1.681132889 -9.98672867 8.90684119 -5.62580033 -5.65213904
## site4 0.861668624 -0.08837356 -0.39844711 -4.66775097 8.36399372
## site5 0.313763560 -1.01588004 1.87767102 2.31770340 5.42516277
## site6 6.529378288 7.39455120 -14.84616499 4.03419235 0.45622761
## site7 -5.633899640 -24.34207194 -5.44065305 -7.18032730 1.82629252
## site8 -12.555033797 -10.58917201 -16.54997133 5.10970094 -3.37561377
## site9 -1.846335244 -1.71583641 -3.90608655 4.18795010 8.04119218
## site10 1.243587225 -8.10385962 22.47498343 10.87071807 -10.32674164
## site11 1.783413258 -0.49895186 8.08309111 12.61004372 -4.22791005
## site12 1.187081397 1.03749989 -2.20274762 -0.81378689 4.51436916
## site13 -1.776921639 -1.57449944 -1.41581988 15.02874839 1.62107349
## site14 1.827500508 1.87546296 -1.12144362 0.59393155 7.82011676
## site15 2.130171068 -0.87232414 6.40073529 -4.17356544 5.37024387
## site16 1.343325121 3.64281560 1.72954020 -1.04464680 2.08610374
## site17 -3.559054125 1.53732153 3.00023979 10.45225279 2.17771813
## site18 0.181786157 1.86543385 0.99214767 -4.97045097 1.81652257
## site19 -3.176068795 3.62807038 -2.34222290 -0.38276460 -2.93054626
## site20 1.487518828 8.16981353 6.77360669 12.69464770 9.58012732
## site21 -2.607202477 4.61050219 -1.77190588 -0.54597527 -5.07366190
## site22 -2.394880629 10.30085583 0.13615614 3.64322571 7.57914769
## site23 -2.713623350 2.23953832 -3.14976010 -6.51777844 -0.13379616
## site24 -0.302631325 2.78494809 -0.55548557 -0.67667195 -0.42263349
## site25 -1.827240522 5.52216488 -3.18481130 4.99407434 -6.44157943
## site26 -2.492641628 4.76874312 0.29311260 -2.01776239 -7.51055346
## site27 -2.826723257 4.06146438 -4.49063360 2.40932300 -4.46647857
## site28 2.769906014 9.28644932 -2.89061951 -10.47527905 -6.05483540
## site29 0.303511607 1.29890762 3.53496253 -2.59325720 1.59467001
## site30 2.862652127 9.16562834 -2.28821298 -4.51365335 -0.01815491
## site31 -1.045564483 -1.40944188 -0.58876204 0.09418159 -1.52744247
## site32 -3.452255135 -2.73553226 -1.72553113 1.61035444 -1.87825190
## site33 1.787458930 -4.72486096 4.10113128 -5.16437954 0.16482646
## site34 0.642397591 -3.88973481 0.53374952 -1.71645780 -1.77556534
## site35 -0.127864901 -2.98662834 -0.99323040 -1.47488837 -0.46094304
## site36 -1.487218508 -2.50048283 -0.55641105 0.63126349 0.59016452
## site37 -1.194235822 -1.50908289 -0.99756627 -0.05460649 -0.73509935
## site38 5.188746719 -3.54316959 4.61870243 -8.69589335 -3.83694887
## site39 -0.499090443 -6.22162446 -1.20542549 0.55849477 -3.83486519
## site40 0.134961010 -1.10483622 -0.17408287 -0.93374634 -2.55904978
## site41 -0.927258020 -3.92290930 -5.52824148 -1.03801502 -0.55065212
## site42 2.210837732 -0.63394383 0.13512765 -0.57885260 -0.47503163
## site43 -30.633299474 10.83552456 11.22212638 -10.13708804 -0.50196796
## site44 0.775444863 -0.21596863 -3.83056461 2.33263719 -0.59314943
## site45 -1.107110833 0.13556768 -0.34443263 1.22530631 -0.44164287
## site46 -0.485045975 0.49800090 0.43557224 0.04293027 -0.87105755
## site47 0.516652723 0.03264460 -0.09397623 -0.24256896 -0.39102195
## site48 3.114389360 -0.22229592 0.96182515 0.58034966 1.18409485
## site49 -1.878664862 0.77463089 -0.49300710 0.01377845 -1.10671109
## site50 -0.003675864 0.03038009 -0.47206215 0.16765819 -0.55193369
## site51 2.534327164 -0.47097653 -0.92362763 2.26628380 -0.79295044
## site52 0.957014267 0.25390026 -0.80557738 0.38924748 -0.65649422
## site53 -0.281170863 -0.12753019 0.61009819 0.72100462 1.00640657
## site54 3.931245184 -0.63938062 1.36652937 -2.09260051 0.12853668
## site55 7.179406196 -1.82930444 1.65737597 0.55591892 4.17916943
## site56 -0.326045013 1.25381228 2.88825748 -2.15949563 0.34893485
## site57 1.922741360 -0.75689092 -2.37545290 -0.95737138 -1.15967290
## site58 0.181391330 0.36484193 -2.96177747 1.25720664 -1.61160788
## site59 0.856382830 0.79501034 -1.27568096 1.76257692 0.10422950
## site60 0.062456208 0.27556783 -0.98979153 0.55237361 -0.20741198
## site61 7.794934316 -1.40423592 3.12658334 -3.91113234 1.90322135
## site62 1.985687331 -1.36574068 -3.13816389 2.92827694 -0.03613436
## site63 1.730070214 -0.48909592 -2.55308110 3.63391577 0.99487633
## site64 2.297258470 -0.19119246 -0.12191020 0.43427371 0.89592614
## site65 2.206132869 -1.58798466 -0.22218648 -1.18655683 -0.42928856
## site66 -0.145926272 0.17798159 0.52045419 -0.87833571 0.19796616
## site67 6.147629392 -0.89149015 1.15031697 -1.05067913 1.11869597
## site68 -9.398443780 -1.33231890 -2.27579327 3.41348234 -0.99832911
## PC11 PC12 PC13 PC14 PC15
## site1 -14.37290566 5.21299481 -5.95679704 4.717395e+00 1.65603740
## site2 -11.63847018 -4.38675595 -0.47381319 -8.939436e+00 0.15878950
## site3 10.71541333 -8.42811981 10.05613904 -7.046066e+00 6.18483766
## site4 1.80751146 -8.21634341 -6.26164212 5.004313e+00 -2.97692306
## site5 4.11925226 -8.43072614 3.58577028 4.194916e+00 -2.61142745
## site6 14.80025474 1.96786024 -5.96529920 9.610562e+00 -5.11835669
## site7 -4.65668243 -0.01611031 -4.78089412 -4.986410e+00 1.52558591
## site8 -2.59786732 4.50044709 -5.48118821 -5.654848e+00 1.08759345
## site9 10.48519601 -1.25842925 4.57456926 2.985273e+00 1.00045909
## site10 1.43666239 -5.51686286 -5.65593177 7.852446e+00 -4.94192686
## site11 4.73506502 22.20648224 -3.65475260 5.314553e+00 4.73425454
## site12 3.55034310 -1.86679770 -5.15119599 2.167117e+00 -0.33785043
## site13 -0.36936031 -9.74859103 -2.72137034 -3.629144e+00 -0.05969533
## site14 7.84509853 -2.21678597 14.55888046 -9.982196e+00 3.88764631
## site15 2.51324790 -3.01197616 -3.64942417 1.823998e+00 1.66016242
## site16 4.94362215 -0.19941396 1.16689765 1.465920e-01 2.07653102
## site17 -9.51208431 -4.54053950 1.49295246 -7.170882e+00 1.59348713
## site18 0.57785012 -4.78494548 -0.63787697 4.296748e+00 -2.40390478
## site19 3.68065414 -2.27340974 3.65412447 -1.387476e+00 2.34479357
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## site53 0.59250430 2.36280224 0.97443333 1.645097e+00 -0.94897887
## site54 1.62291513 -0.58283680 -1.64624243 -9.412461e-01 -1.88817702
## site55 3.90498470 4.53408173 1.53328552 -1.259791e+01 -27.81314626
## site56 1.12965679 2.08683986 -0.31546412 5.135283e+00 8.21955012
## site57 -1.56137848 -0.44078866 -0.05953292 2.875323e+00 2.12367148
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## site59 -0.61330079 -0.63267413 -0.89839293 4.897223e-02 3.39326625
## site60 -0.61415036 0.17999878 1.58931814 1.879232e-01 0.64926676
## site61 3.00958941 -2.79857001 -4.11398520 9.856250e-02 2.64891617
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## site68 1.82940616 -1.98514898 1.16219556 -1.134689e+00 -4.21562017
## PC16 PC17 PC18 PC19 PC20
## site1 5.49630580 -2.0887457 -0.38972240 -0.77485578 -4.6802525
## site2 -3.95033161 -4.3305852 5.32434748 2.13813150 -3.2711524
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## site5 4.63405927 0.9764541 9.08934723 5.73999640 4.5498304
## site6 3.87925100 11.7307680 -2.36272993 -5.77947224 8.5404104
## site7 -2.97511211 0.7655208 -2.45883635 1.84982746 5.0753529
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## site9 0.53717459 -8.7277219 11.41666212 3.09297530 -7.3377755
## site10 -1.44973703 -4.1816204 -4.77540982 2.27698921 14.0710938
## site11 2.12994849 -3.7348783 -2.61212113 1.15571677 -11.0211937
## site12 0.92659801 -2.2960943 -0.83792567 0.21511899 4.1928080
## site13 -7.43602366 -12.3178185 -5.89946418 -16.41778537 -12.0393690
## site14 -10.42584448 -7.2998060 -15.52029485 10.31057009 8.3305774
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## site17 2.54595681 8.6019140 2.59105248 2.22452790 -0.4401765
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## site55 -1.14942902 0.3397144 3.97188461 1.30819522 -3.8273156
## site56 -7.64516378 1.9812179 2.21416393 -0.15403886 -0.2842939
## site57 4.21764388 -0.1591294 -4.03895128 -0.24918824 -1.2591699
## site58 10.55080372 -5.8125053 -4.21861451 0.50654822 2.4662757
## site59 3.22217701 -3.0364319 -0.40937618 1.09860596 1.8909976
## site60 2.34123332 -1.6346622 0.83248157 0.91541552 0.3468963
## site61 -6.76755184 9.0586710 -8.05809776 -8.94999547 -0.8376222
## site62 -4.55836918 2.3479429 3.61384676 2.00370240 0.4017670
## site63 -1.58591917 -0.7454692 6.29217912 4.25992205 1.5341148
## site64 1.45775117 -1.3227433 1.33544784 2.16682482 -0.8307231
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## site68 -1.13846247 1.7466180 -0.75503144 -1.53544367 -1.3351355
## PC21 PC22 PC23 PC24 PC25
## site1 1.52127677 2.565231e+00 2.84867213 -14.51133159 0.61703924
## site2 1.18958045 -2.353871e+00 4.40090903 4.95007638 5.94616020
## site3 6.76569437 -4.099389e+00 -6.54327475 -1.32628232 -4.63202178
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## site8 -1.67380508 -1.772087e+00 1.16230894 2.19537365 4.56303504
## site9 5.17608303 -7.201598e-01 9.96894365 2.00565517 6.17165527
## site10 -4.01785476 -3.918991e+00 4.06441196 -4.76660074 5.45954772
## site11 8.43616499 -3.644659e-01 3.46244451 4.70352924 0.50464610
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## site13 -9.43539663 1.280679e+00 -3.59278229 -5.20667811 -9.60392700
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## site16 -4.10755195 2.860850e+00 -0.03938179 3.10323219 7.23386316
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## site54 0.58936799 2.142771e+00 7.19036001 1.65080290 0.46224481
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## site56 0.96323542 -2.520177e+00 -7.18348633 -1.36642467 0.69877885
## site57 0.91455946 -2.226518e+00 3.98402166 1.85056632 -3.96681927
## site58 -0.57516854 8.398843e-01 4.41692100 0.67361231 -0.73542564
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## site68 0.80968484 1.642903e+00 1.81935236 0.66659776 -0.21505206
## PC26 PC27 PC28 PC29 PC30
## site1 1.74232008 1.93760232 3.06699931 -4.012591148 -0.29814505
## site2 -2.92706227 -0.23479646 -3.02277877 -0.454970690 0.93670158
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## site12 0.49643391 -2.27416917 -1.96938361 3.421484512 -4.88325086
## site13 0.82967506 0.58635148 -2.77695075 -1.641563844 0.44653127
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## PC31 PC32 PC33 PC34 PC35
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## site17 -0.276956012 0.02952841 0.365363659 0.379777361 -0.062911367
## site18 -0.188507826 0.16974967 -0.167991530 -0.551473809 -0.018085397
## site19 -0.478406861 -0.67113133 0.087328167 0.204150946 0.175209247
## site20 0.441325586 -1.33267229 0.048167532 -0.008074330 -0.011842658
## site21 -1.175873410 0.38786324 0.691798172 -0.037769247 -0.182295054
## site22 -0.169491868 -0.17744562 -0.006216448 -0.535166916 0.214770258
## site23 -0.825815900 0.17327368 -0.045200458 0.234586715 0.042754239
## site24 3.552367068 -2.76831047 0.207651921 -0.488751552 0.142597279
## site25 -0.897871020 0.81259289 -0.315976623 0.455844290 0.249353662
## site26 -0.108921723 0.41293028 -0.111758671 -0.830021981 0.200355378
## site27 -0.200586605 0.16590695 0.361157136 -0.166975900 -0.434546376
## site28 0.850390607 0.06563128 -0.319580275 -0.106389542 -0.073132604
## site29 -0.411883621 1.08302245 -0.035881677 -0.253646345 0.401629970
## site30 -0.306930219 0.71433361 0.054607240 -0.276848750 -0.018592157
## site31 7.571247978 -6.86932521 3.424057519 -2.965578607 -0.650374020
## site32 0.240980654 -1.70785851 0.436938747 -0.234637483 0.040409846
## site33 1.546308867 -4.10502138 0.072031601 0.082083631 0.160287796
## site34 0.006295072 1.09216765 -1.065632787 0.524808194 0.438855983
## site35 -0.637917908 -2.55274233 2.356997663 -4.797163403 2.000984400
## site36 -1.355856745 18.81096463 0.592748781 -5.475616784 1.063908525
## site37 -1.149865883 -1.71729962 -1.158899205 0.679576388 -2.329834842
## site38 0.053699549 -0.27291754 -0.042932177 -0.382053004 0.319228742
## site39 -2.549160021 0.55840060 1.709413173 -0.685933265 -0.253158219
## site40 -3.624237518 1.94183863 -8.448411518 15.712499818 -1.588087839
## site41 0.642641303 -1.10690400 0.323517129 -0.129262618 0.177449078
## site42 -1.632751204 0.53149930 0.617890946 -0.146515289 0.255324443
## site43 -0.687085882 -0.19163314 0.224026777 -0.066162495 0.120074209
## site44 -1.069934833 -0.12334657 0.692476866 -0.118396751 -0.565001633
## site45 2.813116578 -3.06318474 -1.896299347 -0.316408030 1.266072076
## site46 1.908172791 2.07316201 9.765091467 3.017269107 -14.647675431
## site47 -3.444928051 0.19570608 13.119035527 7.359372656 10.908409857
## site48 -1.265074750 -0.20151095 -0.815725583 -0.958149148 0.497526186
## site49 3.985760969 -0.34788251 -6.278662244 -2.949273236 3.278379639
## site50 -15.725172534 -4.20787987 -2.402407531 -4.632330658 -2.093535891
## site51 -0.456894683 -0.50857713 -1.381741719 -0.870035665 0.565444392
## site52 2.766307692 -0.91022919 -3.929512751 -0.563586141 0.569383632
## site53 0.605795663 0.77438998 -0.433845355 0.256009804 0.187744266
## site54 2.296701218 0.25702157 0.399316571 0.191932945 -0.014823778
## site55 -1.083897356 -0.11275540 1.356979172 0.500795245 0.718595137
## site56 1.231304778 0.93386651 -0.678334593 0.193441588 1.253838365
## site57 -1.889671636 0.15400513 -0.917752506 0.379389809 -0.658977212
## site58 -1.225942445 -0.45614089 0.136780390 -0.673878649 0.723226887
## site59 0.377286071 0.38168629 0.139708148 -0.895726885 -1.101824921
## site60 11.218402336 3.53389950 -2.363458139 1.960883586 1.262444081
## site61 0.140215098 0.45827265 0.422763010 0.060575088 -0.165582809
## site62 -0.594378722 -0.62107277 0.206793012 -0.255972906 1.395303236
## site63 0.278943158 0.31091884 0.117976809 -0.000383430 0.922427116
## site64 -1.361968658 -0.26290135 -2.279053868 -1.914227031 -1.759624090
## site65 1.159239945 0.91983687 -0.865871696 0.286387862 -1.973457053
## site66 2.985271556 1.02758601 0.336730249 1.010887033 -0.114548818
## site67 -1.182966449 -0.41688257 -0.872646389 -0.728608197 -0.670170726
## site68 -0.729003002 -0.32989353 -0.857546580 -0.072577108 0.597169646
## PC66 PC67 PC68
## site1 0.25887920 -0.071769164 3.892704e-15
## site2 0.12454320 0.105779378 5.526341e-14
## site3 -0.07633258 -0.398583275 5.243886e-15
## site4 -0.11887366 -0.110486552 -1.191202e-14
## site5 0.14307481 0.111953379 3.567405e-14
## site6 -0.05460709 -0.280228888 1.748930e-14
## site7 0.14070545 -0.009829872 3.880435e-14
## site8 -0.28486535 0.046058915 -9.299202e-16
## site9 -0.33603898 0.142422536 6.479185e-15
## site10 -0.30725024 -0.171880869 -2.168946e-15
## site11 -0.15993648 -0.065006735 1.228509e-15
## site12 0.26466599 0.011931880 -1.588681e-15
## site13 0.20906731 0.159979058 -4.903738e-15
## site14 -0.35471265 0.072669611 2.598507e-15
## site15 -0.52384743 0.234050681 2.584506e-15
## site16 0.23303718 -0.330701310 1.701644e-14
## site17 0.08964182 0.124711895 -7.384393e-15
## site18 -0.25471205 0.001137405 1.491405e-14
## site19 -0.01173648 0.259513254 -8.171957e-15
## site20 -0.17733310 0.101960367 -1.365282e-14
## site21 0.24572907 0.088676997 -2.194100e-15
## site22 -0.37554830 -0.180851922 -1.381023e-15
## site23 0.04078429 -0.056599579 6.625544e-15
## site24 -0.19577801 0.123900328 -6.711320e-15
## site25 -0.23297624 0.050166076 1.793521e-15
## site26 -0.02186814 -0.258533612 1.608616e-15
## site27 0.01552896 0.192151439 8.280160e-15
## site28 0.16603277 -0.171118298 -3.667437e-15
## site29 -0.44577941 0.244581121 -6.269291e-15
## site30 -0.18915249 -0.140358994 -6.751652e-15
## site31 -0.17315281 0.436750373 -7.379188e-15
## site32 -0.56424465 0.024196753 -2.902858e-15
## site33 0.66614739 -0.446664222 -2.941022e-15
## site34 0.23730471 -0.192871957 -2.847223e-15
## site35 -7.32245000 1.549152880 -1.166049e-14
## site36 0.37056289 -0.843782712 -3.807393e-15
## site37 14.45098047 -4.535399839 -7.684933e-15
## site38 0.09154836 -0.492126926 4.334975e-16
## site39 -0.00175165 0.343053508 -4.299310e-15
## site40 -3.46059710 0.806501265 -9.001155e-15
## site41 -1.89944043 0.853980998 -1.039154e-14
## site42 5.10164319 15.289799775 -6.909078e-15
## site43 -0.09422860 0.371879861 2.143576e-15
## site44 -0.01493225 0.319309375 1.340106e-14
## site45 -0.07908277 -0.102701236 -8.936103e-15
## site46 -2.04799715 -0.678620421 -7.363266e-15
## site47 0.92650612 -2.167954050 -8.131191e-15
## site48 0.04022664 -0.438351197 -1.670213e-15
## site49 -0.68839872 -1.788985019 -8.169045e-15
## site50 -1.12103605 -2.293986149 -1.578014e-14
## site51 -0.06722644 -0.407967986 4.361419e-14
## site52 -0.54592453 -0.364293408 -1.013306e-14
## site53 0.03159422 0.633428480 2.980038e-15
## site54 -0.48673017 -1.418488567 -4.339086e-15
## site55 0.17039794 -0.395649464 -2.323337e-15
## site56 0.19451684 0.429825683 -1.466120e-14
## site57 -0.21459565 -0.513876793 -6.884792e-15
## site58 -0.05539652 -0.088642855 -1.229626e-14
## site59 -0.45210950 -0.484867380 -2.367482e-14
## site60 0.21320444 -1.082987012 3.104056e-15
## site61 -0.42298422 -0.722907101 -9.144270e-15
## site62 -0.06754894 -0.961661365 -4.450616e-15
## site63 0.24078070 0.147297218 -1.414288e-14
## site64 -0.53609221 -0.011562358 -3.630141e-15
## site65 0.18152187 -1.138407140 -4.290188e-16
## site66 0.13094847 0.095265785 -1.003214e-14
## site67 -0.48154695 0.279380015 -8.675894e-15
## site68 -0.06075828 0.167237939 1.169540e-14Plotting the PCA Data
Using “ggscatter”, the PCA data is plotted showing the relationship between percent variation of PC1 and PC2 with the sample data.
ggpubr::ggscatter(data = pca_scores2,
y = "PC2",
x = "PC1",
color = "pop_id",
shape = "pop_id",
xlab = "PC1 (19.9% variation)",
ylab = "PC2 (2.3% variation)",
main = "PC1 vs PC2 Percent Variation Plot")
There are two distinct clusters in the result of plotting the PCA data. The cluster one consists of the “Div” and the “Cau” tagged samples. These two groups varied highly from the “Alt”, “Nel”, and “Sub”groups that formed cluster two. Cluster one varies highly with PC1, but not highly with PC2. Despite all three groups in cluster two not varying with PC1 very high, the group tagged “Sub” doesn’t seem to vary highly with PC1 or PC2.