# Limpiar entorno
rm(list = ls())
options(encoding = "UTF-8")
# Cargar paquetes
library(readxl)
library(FactoMineR)
library(dplyr)
##
## Adjuntando el paquete: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(factoextra) # <- NECESARIO para fviz_*
## Cargando paquete requerido: ggplot2
## Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
# Leer datos
data <- read_excel("C:/Surco/AFirstWeek/Bases/breastcancer.xlsx")
# Eliminar columna ID si existe
data <- data %>% select(-id)
# Convertir diagnosis a factor
data$diagnosis <- as.factor(data$diagnosis)
# Mover diagnosis al final (para facilitar uso de ncol)
data <- data %>% relocate(diagnosis, .after = last_col())
# Verificar tipos de datos
str(data)
## tibble [569 × 31] (S3: tbl_df/tbl/data.frame)
## $ radius_mean : num [1:569] 18 20.6 19.7 11.4 20.3 ...
## $ texture_mean : num [1:569] 10.4 17.8 21.2 20.4 14.3 ...
## $ perimeter_mean : num [1:569] 122.8 132.9 130 77.6 135.1 ...
## $ area_mean : num [1:569] 1001 1326 1203 386 1297 ...
## $ smoothness_mean : num [1:569] 0.1184 0.0847 0.1096 0.1425 0.1003 ...
## $ compactness_mean : num [1:569] 0.2776 0.0786 0.1599 0.2839 0.1328 ...
## $ concavity_mean : num [1:569] 0.3001 0.0869 0.1974 0.2414 0.198 ...
## $ concave points_mean : num [1:569] 0.1471 0.0702 0.1279 0.1052 0.1043 ...
## $ symmetry_mean : num [1:569] 0.242 0.181 0.207 0.26 0.181 ...
## $ fractal_dimension_mean : num [1:569] 0.0787 0.0567 0.06 0.0974 0.0588 ...
## $ radius_se : num [1:569] 1.095 0.543 0.746 0.496 0.757 ...
## $ texture_se : num [1:569] 0.905 0.734 0.787 1.156 0.781 ...
## $ perimeter_se : num [1:569] 8.59 3.4 4.58 3.44 5.44 ...
## $ area_se : num [1:569] 153.4 74.1 94 27.2 94.4 ...
## $ smoothness_se : num [1:569] 0.0064 0.00522 0.00615 0.00911 0.01149 ...
## $ compactness_se : num [1:569] 0.049 0.0131 0.0401 0.0746 0.0246 ...
## $ concavity_se : num [1:569] 0.0537 0.0186 0.0383 0.0566 0.0569 ...
## $ concave points_se : num [1:569] 0.0159 0.0134 0.0206 0.0187 0.0188 ...
## $ symmetry_se : num [1:569] 0.03 0.0139 0.0225 0.0596 0.0176 ...
## $ fractal_dimension_se : num [1:569] 0.00619 0.00353 0.00457 0.00921 0.00511 ...
## $ radius_worst : num [1:569] 25.4 25 23.6 14.9 22.5 ...
## $ texture_worst : num [1:569] 17.3 23.4 25.5 26.5 16.7 ...
## $ perimeter_worst : num [1:569] 184.6 158.8 152.5 98.9 152.2 ...
## $ area_worst : num [1:569] 2019 1956 1709 568 1575 ...
## $ smoothness_worst : num [1:569] 0.162 0.124 0.144 0.21 0.137 ...
## $ compactness_worst : num [1:569] 0.666 0.187 0.424 0.866 0.205 ...
## $ concavity_worst : num [1:569] 0.712 0.242 0.45 0.687 0.4 ...
## $ concave points_worst : num [1:569] 0.265 0.186 0.243 0.258 0.163 ...
## $ symmetry_worst : num [1:569] 0.46 0.275 0.361 0.664 0.236 ...
## $ fractal_dimension_worst: num [1:569] 0.1189 0.089 0.0876 0.173 0.0768 ...
## $ diagnosis : Factor w/ 2 levels "B","M": 2 2 2 2 2 2 2 2 2 2 ...
# Ejecutar PCA con diagnosis como variable suplementaria
pcacancer <- PCA(data, quali.sup = ncol(data), graph = FALSE)
# Revisar estructura de resultados
str(pcacancer)
## List of 6
## $ eig : num [1:30, 1:3] 13.28 5.69 2.82 1.98 1.65 ...
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : chr [1:30] "comp 1" "comp 2" "comp 3" "comp 4" ...
## .. ..$ : chr [1:3] "eigenvalue" "percentage of variance" "cumulative percentage of variance"
## $ var :List of 4
## ..$ coord : num [1:30, 1:5] 0.798 0.378 0.829 0.805 0.52 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:30] "radius_mean" "texture_mean" "perimeter_mean" "area_mean" ...
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## ..$ cor : num [1:30, 1:5] 0.798 0.378 0.829 0.805 0.52 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:30] "radius_mean" "texture_mean" "perimeter_mean" "area_mean" ...
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## ..$ cos2 : num [1:30, 1:5] 0.636 0.143 0.688 0.649 0.27 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:30] "radius_mean" "texture_mean" "perimeter_mean" "area_mean" ...
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## ..$ contrib: num [1:30, 1:5] 4.79 1.08 5.18 4.88 2.03 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:30] "radius_mean" "texture_mean" "perimeter_mean" "area_mean" ...
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## $ ind :List of 4
## ..$ coord : num [1:569, 1:5] 9.19 2.39 5.73 7.12 3.94 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:569] "1" "2" "3" "4" ...
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## ..$ cos2 : num [1:569, 1:5] 0.737 0.216 0.878 0.259 0.45 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:569] "1" "2" "3" "4" ...
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## ..$ contrib: num [1:569, 1:5] 1.1182 0.0754 0.435 0.6714 0.2049 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:569] "1" "2" "3" "4" ...
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## ..$ dist : Named num [1:569] 10.71 5.13 6.12 13.99 5.87 ...
## .. ..- attr(*, "names")= chr [1:569] "1" "2" "3" "4" ...
## $ svd :List of 3
## ..$ vs: num [1:30] 3.64 2.39 1.68 1.41 1.28 ...
## ..$ U : num [1:569, 1:5] 2.522 0.655 1.573 1.954 1.08 ...
## ..$ V : num [1:30, 1:5] 0.219 0.104 0.228 0.221 0.143 ...
## $ quali.sup:List of 5
## ..$ coord : num [1:2, 1:5] -2.206 3.715 0.346 -0.583 0.213 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:2] "B" "M"
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## ..$ cos2 : num [1:2, 1:5] 0.96032 0.96032 0.02366 0.02366 0.00897 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:2] "B" "M"
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## ..$ v.test: num [1:2, 1:5] -18.72 18.72 4.49 -4.49 3.93 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:2] "B" "M"
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## ..$ dist : Named num [1:2] 2.25 3.79
## .. ..- attr(*, "names")= chr [1:2] "B" "M"
## ..$ eta2 : num [1, 1:5] 0.617 0.03548 0.02715 0.01627 0.00986
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr "diagnosis"
## .. .. ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
## $ call :List of 10
## ..$ row.w : num [1:569] 0.00176 0.00176 0.00176 0.00176 0.00176 ...
## ..$ col.w : num [1:30] 1 1 1 1 1 1 1 1 1 1 ...
## ..$ scale.unit: logi TRUE
## ..$ ncp : num 5
## ..$ centre : num [1:30] 14.1273 19.2896 91.969 654.8891 0.0964 ...
## ..$ ecart.type: num [1:30] 3.521 4.2973 24.2776 351.6048 0.0141 ...
## ..$ X :'data.frame': 569 obs. of 31 variables:
## .. ..$ radius_mean : num [1:569] 18 20.6 19.7 11.4 20.3 ...
## .. ..$ texture_mean : num [1:569] 10.4 17.8 21.2 20.4 14.3 ...
## .. ..$ perimeter_mean : num [1:569] 122.8 132.9 130 77.6 135.1 ...
## .. ..$ area_mean : num [1:569] 1001 1326 1203 386 1297 ...
## .. ..$ smoothness_mean : num [1:569] 0.1184 0.0847 0.1096 0.1425 0.1003 ...
## .. ..$ compactness_mean : num [1:569] 0.2776 0.0786 0.1599 0.2839 0.1328 ...
## .. ..$ concavity_mean : num [1:569] 0.3001 0.0869 0.1974 0.2414 0.198 ...
## .. ..$ concave points_mean : num [1:569] 0.1471 0.0702 0.1279 0.1052 0.1043 ...
## .. ..$ symmetry_mean : num [1:569] 0.242 0.181 0.207 0.26 0.181 ...
## .. ..$ fractal_dimension_mean : num [1:569] 0.0787 0.0567 0.06 0.0974 0.0588 ...
## .. ..$ radius_se : num [1:569] 1.095 0.543 0.746 0.496 0.757 ...
## .. ..$ texture_se : num [1:569] 0.905 0.734 0.787 1.156 0.781 ...
## .. ..$ perimeter_se : num [1:569] 8.59 3.4 4.58 3.44 5.44 ...
## .. ..$ area_se : num [1:569] 153.4 74.1 94 27.2 94.4 ...
## .. ..$ smoothness_se : num [1:569] 0.0064 0.00522 0.00615 0.00911 0.01149 ...
## .. ..$ compactness_se : num [1:569] 0.049 0.0131 0.0401 0.0746 0.0246 ...
## .. ..$ concavity_se : num [1:569] 0.0537 0.0186 0.0383 0.0566 0.0569 ...
## .. ..$ concave points_se : num [1:569] 0.0159 0.0134 0.0206 0.0187 0.0188 ...
## .. ..$ symmetry_se : num [1:569] 0.03 0.0139 0.0225 0.0596 0.0176 ...
## .. ..$ fractal_dimension_se : num [1:569] 0.00619 0.00353 0.00457 0.00921 0.00511 ...
## .. ..$ radius_worst : num [1:569] 25.4 25 23.6 14.9 22.5 ...
## .. ..$ texture_worst : num [1:569] 17.3 23.4 25.5 26.5 16.7 ...
## .. ..$ perimeter_worst : num [1:569] 184.6 158.8 152.5 98.9 152.2 ...
## .. ..$ area_worst : num [1:569] 2019 1956 1709 568 1575 ...
## .. ..$ smoothness_worst : num [1:569] 0.162 0.124 0.144 0.21 0.137 ...
## .. ..$ compactness_worst : num [1:569] 0.666 0.187 0.424 0.866 0.205 ...
## .. ..$ concavity_worst : num [1:569] 0.712 0.242 0.45 0.687 0.4 ...
## .. ..$ concave points_worst : num [1:569] 0.265 0.186 0.243 0.258 0.163 ...
## .. ..$ symmetry_worst : num [1:569] 0.46 0.275 0.361 0.664 0.236 ...
## .. ..$ fractal_dimension_worst: num [1:569] 0.1189 0.089 0.0876 0.173 0.0768 ...
## .. ..$ diagnosis : Factor w/ 2 levels "B","M": 2 2 2 2 2 2 2 2 2 2 ...
## ..$ row.w.init: num [1:569] 1 1 1 1 1 1 1 1 1 1 ...
## ..$ call : language PCA(X = data, quali.sup = ncol(data), graph = FALSE)
## ..$ quali.sup :List of 5
## .. ..$ quali.sup :'data.frame': 569 obs. of 1 variable:
## .. .. ..$ diagnosis: Factor w/ 2 levels "B","M": 2 2 2 2 2 2 2 2 2 2 ...
## .. ..$ modalite : int 2
## .. ..$ nombre : num [1:2] 357 212
## .. ..$ barycentre:'data.frame': 2 obs. of 30 variables:
## .. .. ..$ radius_mean : num [1:2] 12.1 17.5
## .. .. ..$ texture_mean : num [1:2] 17.9 21.6
## .. .. ..$ perimeter_mean : num [1:2] 78.1 115.4
## .. .. ..$ area_mean : num [1:2] 463 978
## .. .. ..$ smoothness_mean : num [1:2] 0.0925 0.1029
## .. .. ..$ compactness_mean : num [1:2] 0.0801 0.1452
## .. .. ..$ concavity_mean : num [1:2] 0.0461 0.1608
## .. .. ..$ concave points_mean : num [1:2] 0.0257 0.088
## .. .. ..$ symmetry_mean : num [1:2] 0.174 0.193
## .. .. ..$ fractal_dimension_mean : num [1:2] 0.0629 0.0627
## .. .. ..$ radius_se : num [1:2] 0.284 0.609
## .. .. ..$ texture_se : num [1:2] 1.22 1.21
## .. .. ..$ perimeter_se : num [1:2] 2 4.32
## .. .. ..$ area_se : num [1:2] 21.1 72.7
## .. .. ..$ smoothness_se : num [1:2] 0.0072 0.00678
## .. .. ..$ compactness_se : num [1:2] 0.0214 0.0323
## .. .. ..$ concavity_se : num [1:2] 0.026 0.0418
## .. .. ..$ concave points_se : num [1:2] 0.00986 0.01506
## .. .. ..$ symmetry_se : num [1:2] 0.0206 0.0205
## .. .. ..$ fractal_dimension_se : num [1:2] 0.00364 0.00406
## .. .. ..$ radius_worst : num [1:2] 13.4 21.1
## .. .. ..$ texture_worst : num [1:2] 23.5 29.3
## .. .. ..$ perimeter_worst : num [1:2] 87 141
## .. .. ..$ area_worst : num [1:2] 559 1422
## .. .. ..$ smoothness_worst : num [1:2] 0.125 0.145
## .. .. ..$ compactness_worst : num [1:2] 0.183 0.375
## .. .. ..$ concavity_worst : num [1:2] 0.166 0.451
## .. .. ..$ concave points_worst : num [1:2] 0.0744 0.1822
## .. .. ..$ symmetry_worst : num [1:2] 0.27 0.323
## .. .. ..$ fractal_dimension_worst: num [1:2] 0.0794 0.0915
## .. ..$ numero : int 31
## - attr(*, "class")= chr [1:2] "PCA" "list"
pcacancer$eig # Varianza explicada
## eigenvalue percentage of variance cumulative percentage of variance
## comp 1 1.328161e+01 4.427203e+01 44.27203
## comp 2 5.691355e+00 1.897118e+01 63.24321
## comp 3 2.817949e+00 9.393163e+00 72.63637
## comp 4 1.980640e+00 6.602135e+00 79.23851
## comp 5 1.648731e+00 5.495768e+00 84.73427
## comp 6 1.207357e+00 4.024522e+00 88.75880
## comp 7 6.752201e-01 2.250734e+00 91.00953
## comp 8 4.766171e-01 1.588724e+00 92.59825
## comp 9 4.168948e-01 1.389649e+00 93.98790
## comp 10 3.506935e-01 1.168978e+00 95.15688
## comp 11 2.939157e-01 9.797190e-01 96.13660
## comp 12 2.611614e-01 8.705379e-01 97.00714
## comp 13 2.413575e-01 8.045250e-01 97.81166
## comp 14 1.570097e-01 5.233657e-01 98.33503
## comp 15 9.413497e-02 3.137832e-01 98.64881
## comp 16 7.986280e-02 2.662093e-01 98.91502
## comp 17 5.939904e-02 1.979968e-01 99.11302
## comp 18 5.261878e-02 1.753959e-01 99.28841
## comp 19 4.947759e-02 1.649253e-01 99.45334
## comp 20 3.115940e-02 1.038647e-01 99.55720
## comp 21 2.997289e-02 9.990965e-02 99.65711
## comp 22 2.743940e-02 9.146468e-02 99.74858
## comp 23 2.434084e-02 8.113613e-02 99.82971
## comp 24 1.805501e-02 6.018336e-02 99.88990
## comp 25 1.548127e-02 5.160424e-02 99.94150
## comp 26 8.177640e-03 2.725880e-02 99.96876
## comp 27 6.900464e-03 2.300155e-02 99.99176
## comp 28 1.589338e-03 5.297793e-03 99.99706
## comp 29 7.488031e-04 2.496010e-03 99.99956
## comp 30 1.330448e-04 4.434827e-04 100.00000
pcacancer$var$coord # Coordenadas de variables
## Dim.1 Dim.2 Dim.3 Dim.4
## radius_mean 0.79776675 -0.55790267 -0.014321182 -0.058276998
## texture_mean 0.37801323 -0.14243819 0.108358294 0.848703801
## perimeter_mean 0.82923555 -0.51334871 -0.015635546 -0.059085011
## area_mean 0.80539280 -0.55126955 0.048177170 -0.075200175
## smoothness_mean 0.51965303 0.44400165 -0.175072188 -0.224307700
## compactness_mean 0.87205011 0.36236113 -0.124375651 -0.044746177
## concavity_mean 0.94171317 0.14353386 0.004589225 -0.026912451
## concave points_mean 0.95065387 -0.08294330 -0.042912871 -0.091950691
## symmetry_mean 0.50353484 0.45410669 -0.067549766 -0.094468500
## fractal_dimension_mean 0.23456539 0.87452298 -0.037894555 -0.068378695
## radius_se 0.75066782 -0.25181113 0.450692931 -0.137837831
## texture_se 0.06351460 0.21466057 0.628888081 0.506443503
## perimeter_se 0.77015490 -0.21341419 0.447610850 -0.125243679
## area_se 0.73933688 -0.36331782 0.362604709 -0.152282609
## smoothness_se 0.05295834 0.48770074 0.518440202 -0.062858236
## compactness_se 0.62098087 0.55518008 0.259824807 0.038659071
## concavity_se 0.55974171 0.47046874 0.296225233 -0.001853314
## concave points_se 0.66844526 0.31090241 0.377126990 -0.104238834
## symmetry_se 0.15488099 0.43859809 0.484439170 -0.062026732
## fractal_dimension_se 0.37379938 0.66820323 0.355046033 -0.021539174
## radius_worst 0.83090957 -0.52452555 -0.079748785 -0.021697488
## texture_worst 0.38072738 -0.10846933 -0.071004288 0.890583627
## perimeter_worst 0.86240823 -0.47684117 -0.081493799 -0.019425394
## area_worst 0.81951682 -0.52329808 -0.019980121 -0.036443035
## smoothness_worst 0.46630955 0.41105891 -0.436115698 -0.024842887
## compactness_worst 0.76567217 0.34256392 -0.396294196 0.128531255
## concavity_worst 0.83371903 0.23370868 -0.290506982 0.104075362
## concave points_worst 0.91432733 -0.01969892 -0.285952302 -0.008453959
## symmetry_worst 0.44791263 0.33848486 -0.455445686 0.051017498
## fractal_dimension_worst 0.48027261 0.65686526 -0.390780903 0.108441378
## Dim.5
## radius_mean -0.048518775
## texture_mean 0.063519440
## perimeter_mean -0.047990153
## area_mean -0.013265627
## smoothness_mean 0.468784268
## compactness_mean -0.015028239
## concavity_mean -0.110908536
## concave points_mean 0.056318830
## symmetry_mean 0.392837675
## fractal_dimension_mean 0.057042168
## radius_se 0.198326624
## texture_se 0.246084813
## perimeter_se 0.155354955
## area_se 0.163809274
## smoothness_se 0.297979065
## compactness_se -0.359487239
## concavity_se -0.454523281
## concave points_se -0.251089422
## symmetry_se 0.324690835
## fractal_dimension_se -0.338081553
## radius_worst 0.005658192
## texture_worst 0.119264982
## perimeter_worst -0.009571346
## area_worst 0.035170715
## smoothness_worst 0.416584530
## compactness_worst -0.156400009
## concavity_worst -0.242063518
## concave points_worst -0.055639634
## symmetry_worst 0.314020423
## fractal_dimension_worst -0.121242324
pcacancer$var$cos2 # Coseno cuadrado
## Dim.1 Dim.2 Dim.3 Dim.4
## radius_mean 0.636431794 0.3112553921 2.050963e-04 3.396209e-03
## texture_mean 0.142894003 0.0202886376 1.174152e-02 7.202981e-01
## perimeter_mean 0.687631593 0.2635268968 2.444703e-04 3.491038e-03
## area_mean 0.648657563 0.3038981121 2.321040e-03 5.655066e-03
## smoothness_mean 0.270039269 0.1971374667 3.065027e-02 5.031394e-02
## compactness_mean 0.760471394 0.1313055907 1.546930e-02 2.002220e-03
## concavity_mean 0.886823686 0.0206019688 2.106098e-05 7.242800e-04
## concave points_mean 0.903742788 0.0068795905 1.841514e-03 8.454930e-03
## symmetry_mean 0.253547334 0.2062128847 4.562971e-03 8.924298e-03
## fractal_dimension_mean 0.055020924 0.7647904383 1.435997e-03 4.675646e-03
## radius_se 0.563502171 0.0634088430 2.031241e-01 1.899927e-02
## texture_se 0.004034105 0.0460791599 3.955002e-01 2.564850e-01
## perimeter_se 0.593138575 0.0455456160 2.003555e-01 1.568598e-02
## area_se 0.546619028 0.1319998412 1.314822e-01 2.318999e-02
## smoothness_se 0.002804585 0.2378520114 2.687802e-01 3.951158e-03
## compactness_se 0.385617244 0.3082249180 6.750893e-02 1.494524e-03
## concavity_se 0.313310781 0.2213408352 8.774939e-02 3.434773e-06
## concave points_se 0.446819069 0.0966603104 1.422248e-01 1.086573e-02
## symmetry_se 0.023988122 0.1923682816 2.346813e-01 3.847315e-03
## fractal_dimension_se 0.139725975 0.4464955533 1.260577e-01 4.639360e-04
## radius_worst 0.690410709 0.2751270525 6.359869e-03 4.707810e-04
## texture_worst 0.144953341 0.0117655963 5.041609e-03 7.931392e-01
## perimeter_worst 0.743747963 0.2273775048 6.641239e-03 3.773459e-04
## area_worst 0.671607821 0.2738408793 3.992052e-04 1.328095e-03
## smoothness_worst 0.217444594 0.1689694296 1.901969e-01 6.171690e-04
## compactness_worst 0.586253867 0.1173500374 1.570491e-01 1.652028e-02
## concavity_worst 0.695087414 0.0546197464 8.439431e-02 1.083168e-02
## concave points_worst 0.835994467 0.0003880475 8.176872e-02 7.146943e-05
## symmetry_worst 0.200625723 0.1145720030 2.074308e-01 2.602785e-03
## fractal_dimension_worst 0.230661782 0.4314719683 1.527097e-01 1.175953e-02
## Dim.5
## radius_mean 2.354072e-03
## texture_mean 4.034719e-03
## perimeter_mean 2.303055e-03
## area_mean 1.759769e-04
## smoothness_mean 2.197587e-01
## compactness_mean 2.258480e-04
## concavity_mean 1.230070e-02
## concave points_mean 3.171811e-03
## symmetry_mean 1.543214e-01
## fractal_dimension_mean 3.253809e-03
## radius_se 3.933345e-02
## texture_se 6.055773e-02
## perimeter_se 2.413516e-02
## area_se 2.683348e-02
## smoothness_se 8.879152e-02
## compactness_se 1.292311e-01
## concavity_se 2.065914e-01
## concave points_se 6.304590e-02
## symmetry_se 1.054241e-01
## fractal_dimension_se 1.142991e-01
## radius_worst 3.201514e-05
## texture_worst 1.422414e-02
## perimeter_worst 9.161067e-05
## area_worst 1.236979e-03
## smoothness_worst 1.735427e-01
## compactness_worst 2.446096e-02
## concavity_worst 5.859475e-02
## concave points_worst 3.095769e-03
## symmetry_worst 9.860883e-02
## fractal_dimension_worst 1.469970e-02
pcacancer$var$contrib # Contribución
## Dim.1 Dim.2 Dim.3 Dim.4
## radius_mean 4.79182799 5.468915807 0.007278210 1.714702e-01
## texture_mean 1.07587881 0.356481698 0.416669002 3.636693e+01
## perimeter_mean 5.17732197 4.630301829 0.008675469 1.762581e-01
## area_mean 4.88387836 5.339644650 0.082366279 2.855170e-01
## smoothness_mean 2.03318209 3.463805721 1.087680124 2.540287e+00
## compactness_mean 5.72574806 2.307106121 0.548956087 1.010895e-01
## concavity_mean 6.67708087 0.361987088 0.000747387 3.656797e-02
## concave points_mean 6.80446833 0.120877909 0.065349461 4.268786e-01
## symmetry_mean 1.90901086 3.623265438 0.161925247 4.505763e-01
## fractal_dimension_mean 0.41426404 13.437757622 0.050958953 2.360674e-01
## radius_se 4.24272561 1.114125676 7.208225536 9.592487e-01
## texture_se 0.03037362 0.809634314 14.035038303 1.294960e+01
## perimeter_se 4.46586429 0.800259675 7.109975188 7.919650e-01
## area_se 4.11560890 2.319304458 4.665882031 1.170833e+00
## smoothness_se 0.02111631 4.179181013 9.538151522 1.994889e-01
## compactness_se 2.90339282 5.415668834 2.395676105 7.545659e-02
## concavity_se 2.35898235 3.889071235 3.113945256 1.734173e-04
## concave points_se 3.36419415 1.698370898 5.047102257 5.485970e-01
## symmetry_se 0.18061158 3.380008708 8.328089385 1.942460e-01
## fractal_dimension_se 1.05202607 7.845154337 4.473384240 2.342354e-02
## radius_worst 5.19824652 4.834122475 0.225691410 2.376913e-02
## texture_worst 1.09138400 0.206727521 0.178910581 4.004458e+01
## perimeter_worst 5.59983385 3.995138596 0.235676347 1.905171e-02
## area_worst 5.05667565 4.811523757 0.014166518 6.705380e-02
## smoothness_worst 1.63718579 2.968878960 6.749479988 3.116007e-02
## compactness_worst 4.41402789 2.061899941 5.573170087 8.340879e-01
## concavity_worst 5.23345841 0.959696770 2.994884133 5.468777e-01
## concave points_worst 6.29437706 0.006818193 2.901710407 3.608400e-03
## symmetry_worst 1.51055300 2.013088461 7.361054968 1.314113e-01
## fractal_dimension_worst 1.73670076 7.581182296 5.419179518 5.937237e-01
## Dim.5
## radius_mean 0.142780853
## texture_mean 0.244716717
## perimeter_mean 0.139686545
## area_mean 0.010673476
## smoothness_mean 13.328963320
## compactness_mean 0.013698294
## concavity_mean 0.746071176
## concave points_mean 0.192378954
## symmetry_mean 9.360015755
## fractal_dimension_mean 0.197352378
## radius_se 2.385680908
## texture_se 3.672991628
## perimeter_se 1.463863342
## area_se 1.627523570
## smoothness_se 5.385447803
## compactness_se 7.838216812
## concavity_se 12.530332072
## concave points_se 3.823905492
## symmetry_se 6.394261226
## fractal_dimension_se 6.932554069
## radius_worst 0.001941805
## texture_worst 0.862732602
## perimeter_worst 0.005556437
## area_worst 0.075026157
## smoothness_worst 10.525835817
## compactness_worst 1.483624039
## concavity_worst 3.553931037
## concave points_worst 0.187766818
## symmetry_worst 5.980893978
## fractal_dimension_worst 0.891576921
# Individuos
head(pcacancer$ind$coord)
## Dim.1 Dim.2 Dim.3 Dim.4 Dim.5
## 1 9.192837 1.948583 -1.1231662 -3.6337309 1.1951101
## 2 2.387802 -3.768172 -0.5292927 -1.1182639 -0.6217750
## 3 5.733896 -1.075174 -0.5517476 -0.9120827 0.1770859
## 4 7.122953 10.275589 -3.2327895 -0.1525470 2.9608784
## 5 3.935302 -1.948072 1.3897667 -2.9406393 -0.5467474
## 6 2.380247 3.949929 -2.9348768 -0.9410369 1.0560419
head(pcacancer$ind$cos2)
## Dim.1 Dim.2 Dim.3 Dim.4 Dim.5
## 1 0.7366868 0.03309951 0.010996938 0.1151037016 0.0124508677
## 2 0.2164877 0.53913561 0.010637227 0.0474815863 0.0146792249
## 3 0.8781764 0.03087731 0.008131356 0.0222203296 0.0008376258
## 4 0.2593764 0.53978871 0.053427543 0.0001189646 0.0448178978
## 5 0.4498315 0.11023095 0.056101900 0.2511755035 0.0086829482
## 6 0.1722700 0.47439927 0.261905853 0.0269264275 0.0339099994
head(pcacancer$ind$contrib)
## Dim.1 Dim.2 Dim.3 Dim.4 Dim.5
## 1 1.11824300 0.11724921 0.07867607 1.171622241 0.152248808
## 2 0.07544555 0.43846352 0.01747215 0.110961077 0.041210182
## 3 0.43504757 0.03569681 0.01898609 0.073815998 0.003342766
## 4 0.67136279 3.26051009 0.65179267 0.002064855 0.934499758
## 5 0.20492419 0.11718767 0.12045877 0.767300731 0.031864823
## 6 0.07496891 0.48178208 0.53719796 0.078576986 0.118877695
# Gráfico de varianza explicada
fviz_eig(pcacancer, addlabels = TRUE, ylim = c(0, 80))
# Variables: contribución y calidad de representación
fviz_pca_var(pcacancer, arrowsize = 1, labelsize = 4, repel = TRUE)
fviz_cos2(pcacancer, choice = "var", axes = 1:2, ylim = c(0, 1.0))
fviz_contrib(pcacancer, choice = "var", axes = 1, top = 15)
# Índice de malignidad: coordenada sobre el primer componente
data$indice_malignidad <- pcacancer$ind$coord[, 1]
# Boxplot para evaluar el índice por diagnóstico
boxplot(indice_malignidad ~ diagnosis, data = data,
main = "Indice de Malignidad segun Diagnostico",
col = c("skyblue", "salmon"))
# Biplot con individuos y variables
fviz_pca_biplot(pcacancer,
geom.ind = "point",
col.ind = data$diagnosis,
palette = "jco",
addEllipses = TRUE,
label = "var",
col.var = "black",
repel = TRUE,
legend.title = "Diagnostico") # sin tilde por seguridad
