Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
## -----------------------------------------------------------------------------
library(aweSOM)
full.data <- iris
## Select variables
train.data <- full.data[, c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")]
### Scale training data
train.data <- scale(train.data)
### RNG Seed (for reproducibility)
set.seed(1465)
### Initialization (PCA grid)
init <- somInit(train.data, 4, 4)
## Train SOM
iris.som <- kohonen::som(train.data, grid = kohonen::somgrid(4, 4, "hexagonal"),
rlen = 100, alpha = c(0.05, 0.01), radius = c(2.65,-2.65),
dist.fcts = "sumofsquares", init = init)
## -----------------------------------------------------------------------------
somQuality(iris.som, train.data)
## -----------------------------------------------------------------------------
superclust_pam <- cluster::pam(iris.som$codes[[1]], 3)
superclasses_pam <- superclust_pam$clustering
superclust_hclust <- hclust(dist(iris.som$codes[[1]]), "complete")
superclasses_hclust <- cutree(superclust_hclust, 3)
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "Cloud", data = full.data,
variables = c("Species", "Sepal.Length", "Sepal.Width",
"Petal.Length", "Petal.Width"),
superclass = superclasses_pam)
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "Hitmap", superclass = superclasses_pam)
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "UMatrix", superclass = superclasses_pam)
## ---- fig.width=8, fig.height=7-----------------------------------------------
aweSOMsmoothdist(iris.som)
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "Circular", data = full.data,
variables = c("Sepal.Length", "Sepal.Width",
"Petal.Length", "Petal.Width"),
superclass = superclasses_pam)
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "Barplot", data = full.data,
variables = c("Sepal.Length", "Sepal.Width",
"Petal.Length", "Petal.Width"),
superclass = superclasses_pam,
values = "prototypes")
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "Boxplot", data = full.data,
variables = c("Sepal.Length", "Sepal.Width",
"Petal.Length", "Petal.Width"),
superclass = superclasses_pam,
scales = "same")
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "Line", data = full.data,
variables = c("Sepal.Length", "Sepal.Width",
"Petal.Length", "Petal.Width"),
superclass = superclasses_pam,
values = "median")
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "Radar", data = full.data,
variables = c("Sepal.Length", "Sepal.Width",
"Petal.Length", "Petal.Width"),
superclass = superclasses_pam)
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "Color", data = full.data,
variables = "Sepal.Length", superclass = superclasses_pam)
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "CatBarplot", data = full.data,
variables = "Species", superclass = superclasses_pam)
## -----------------------------------------------------------------------------
aweSOMplot(som = iris.som, type = "Pie", data = full.data, variables = "Species",
superclass = superclasses_pam)
## ---- fig.width=7, fig.height=4-----------------------------------------------
aweSOMscreeplot(som = iris.som, method = "pam", nclass = 3)
## ---- fig.width=7, fig.height=6-----------------------------------------------
aweSOMsilhouette(iris.som, superclasses_pam)
## ---- fig.width=7, fig.height=4-----------------------------------------------
aweSOMdendrogram(clust = superclust_hclust, nclass = 3)
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