I have built a cluster plot with fviz_cluster. shown in attached image.
fviz_cluster(hcpc, palette = c("blue", "red", "black"),
ellipse.type = "convex", # Concentration ellipse
star.plot = TRUE, # Add segments from centroids to items
repel = TRUE, # Avoid label overplotting (slow)
ggtheme = theme_minimal())
pca <- PCA(data.frame(data, row.names = 1), ncp = Inf, graph = TRUE, scale.unit = TRUE)
I want to add variables in the cluster plot to show a relation of respective variable with the cluster on which basis these are constrcted by HCPC function.
hcpc <- HCPC(pca,method = "ward", metric= "euclidean",consol=FALSE, graph=TRUE,
graph.scale = "sqrt_inertia",order = T)
dataset is a as follows
| Genotype | var1 | var2 | var3 | var4 | var5 | var6 | var7 | var8 | var9 | var10 | var11 | var12 | var13 | var14 | var15 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| sp1 | 1.637918 | 16.495 | 0.77675 | 7.477917 | -0.01383 | -0.26151 | -0.23293 | 0.292033 | 0.485567 | 0.5669 | 0.392739 | 99.52778 | -1.17835 | 0.229556 | -0.39866 |
| sp2 | -0.32645 | 16.63333 | 1.037769 | 7.933333 | 0.3822 | -0.44884 | -0.43737 | 0.2689 | 0.474 | 0.516167 | 0.379568 | 98.66667 | -0.12126 | -1.33545 | -1.23918 |
| sp3 | -0.36778 | 12.60417 | 0.169904 | 5.3975 | -0.55788 | -0.07758 | 0.084623 | 0.146567 | 0.629067 | 0.332833 | -0.74823 | 103.75 | -0.45396 | -1.09686 | -0.71563 |
| sp4 | -1.04965 | 15.9 | 0.295659 | 7.053333 | -0.2199 | -0.26855 | 0.194102 | 0.2245 | 0.557733 | 0.472933 | -0.23829 | 92.33333 | -0.75625 | -1.33545 | -1.23918 |
| sp5 | 0.674863 | 10.76 | -0.34865 | 5.046667 | -0.45314 | -0.17183 | 0.499055 | 0.2295 | 0.481067 | 0.470433 | -0.40215 | 71 | -0.75752 | -1.33545 | -1.23918 |
| sp6 | -1.187 | 9.033333 | -0.63144 | 3.826667 | -0.64804 | -0.99823 | -0.73975 | 0.180933 | 0.260633 | 0.3383 | -1.09673 | 108.6667 | -0.82717 | -1.33545 | -1.23918 |
| sp7 | -0.03838 | 5.406667 | -1.32602 | 1.091 | -1.34433 | 1.367319 | 1.43931 | 0.158867 | 0.578267 | 0.350567 | -0.55303 | 88.66667 | 0.391606 | -0.11855 | 0.625054 |
| sp8 | -0.33247 | 11.2025 | -0.13444 | 4.6475 | -0.26406 | 0.023718 | 0.282222 | 0.168533 | 0.544867 | 0.3375 | 0.560527 | 43.55556 | -1.18273 | -0.65414 | -0.28142 |
| sp9 | 0.283242 | 12.36 | -0.20031 | 5.233333 | -0.42353 | -0.03327 | 0.46696 | 0.216133 | 0.488833 | 0.4381 | -0.38686 | 87.66667 | -0.48168 | 0.560739 | -0.60173 |
| sp10 | 0.473607 | 11.06 | -0.19594 | 5.197333 | -0.31603 | -0.08682 | 0.270725 | 0.190367 | 0.5792 | 0.433367 | -1.07407 | 71.33333 | -0.22937 | -0.49644 | -0.43777 |
| sp11 | 1.506141 | 17.53333 | 0.421256 | 7.62 | -0.20013 | -0.2023 | 0.187563 | 0.253067 | 0.4451 | 0.5073 | -0.72271 | 44 | -1.43844 | 0.833085 | -0.54608 |
| sp12 | 0.826359 | 12.01333 | -0.15668 | 5.438 | -0.68214 | 0.186844 | 0.702316 | 0.234733 | 0.472267 | 0.462133 | -0.13121 | 79.33333 | 0.26208 | 0.343665 | -0.18439 |
| sp13 | -0.81205 | 8.366667 | -0.82383 | 2.94 | -0.70493 | 0.448508 | 0.793381 | 0.1573 | 0.683033 | 0.398533 | -1.2223 | 79.66667 | -0.51911 | -0.70502 | -0.34878 |
| sp14 | 0.15826 | 12.32 | -0.23267 | 4.966667 | -0.47136 | 0.160231 | 0.513613 | 0.2562 | 0.467867 | 0.501533 | -0.26897 | 157.3333 | 0.683273 | -0.49121 | 0.340543 |
| sp15 | 0.841028 | 17.06667 | 0.436611 | 7.23 | -0.22218 | -0.0743 | 0.171861 | 0.214567 | 0.538033 | 0.4394 | -0.12116 | 128.3333 | 0.378802 | 0.015846 | 0.526323 |
| sp16 | -0.37529 | 6.403333 | -1.12965 | 1.942333 | -1.04587 | 0.774613 | 1.105434 | 0.118233 | 0.603967 | 0.36925 | -0.67939 | 102.3333 | -0.5009 | 0.622995 | 0.728144 |
| sp17 | 0.425415 | 8.96 | -0.86026 | 2.857333 | -1.00362 | 0.714724 | 1.103843 | 0.2048 | 0.481733 | 0.4071 | -0.11519 | 118 | -0.06422 | 0.14123 | 0.264738 |
| sp18 | 0.409411 | 11.30333 | -0.52009 | 4.11 | -0.63759 | 0.517846 | 0.702689 | 0.143367 | 0.598533 | 0.352433 | -1.42041 | 55 | -0.60815 | -0.50147 | 0.351138 |
| sp19 | 2.260841 | 10.61333 | -0.50895 | 4.044 | -1.17319 | 1.015295 | 1.126482 | 0.223133 | 0.559833 | 0.442733 | 0.464186 | 129.6667 | 0.268648 | 0.007618 | 0.538839 |
| sp20 | 1.288929 | 7.223333 | -0.90727 | 1.138667 | -1.59676 | 1.704387 | 0.880127 | 0.098067 | 0.618433 | 0.2325 | -1.81553 | 145.6667 | -0.05645 | 0.851715 | 0.37077 |
| sp21 | -0.4669 | 7.194167 | -1.03123 | 1.9675 | -1.42041 | 0.958772 | 1.070749 | 0.108933 | 0.5125 | 0.227667 | -0.50591 | 144.9167 | 0.56866 | 0.32833 | 1.275744 |
| sp22 | -0.51754 | 6.656667 | -1.33466 | 1.080667 | -1.58034 | 1.576634 | 1.683792 | 0.172667 | 0.632233 | 0.3988 | -0.71183 | 145 | 0.705613 | 0.503667 | 0.876036 |
| sp23 | 0.562136 | 9.703333 | -0.73487 | 3.222333 | -0.96489 | 0.817607 | 1.050613 | 0.165233 | 0.534833 | 0.335733 | 0.215271 | 223.6667 | 1.571329 | -1.14217 | -0.46953 |
| sp24 | 0.133826 | 7.99 | -1.15028 | 1.643333 | -1.16784 | 1.243086 | 1.278266 | 0.176967 | 0.532233 | 0.3476 | 0.503408 | 87.33333 | -0.38446 | 0.610718 | 0.120317 |