k means - Get clusters from PCA r -
i have pca shows 2 big clusters , dont know how figure out of samples in each cluster.
if helps, im using prcomp generate pca:
pca1 <- autoplot(prcomp(df), label = true, label.size = 2)
my approach has been attempt cluster pca output using kmeans 2 groups clusters:
pca <- prcomp(df, scale.=true) clust <- kmeans(pca$x[,1:2], centers=2)$cluster
i can make beautiful plot, still lost samples in each cluster. reference, here plot generate if graph kmeans output:
as can see in first pca plot, labels literally sample each dot is. ideal output 2 column txt file sample name in 1 column, , group belongs in other column.
all aside, if there better way, please let me know.
thanks in advance.
here chunk of data:
b c b e sample_1013 312011 624559 625898 534309 220415 sample_1046 474774 949458 951145 843049 366136 sample_104 645363 1290450 1292520 919474 272200 sample_1057 267319 534685 535294 690574 422645 sample_106 414065 830571 834527 657354 234130 sample_107 299289 602483 603756 566256 262153
in question, clust name of output kmeans:
clust <- kmeans(pca$x[,1:2], centers=2)$cluster
i typed clust terminal , got samples belong each group:
> clust sample_1013 sample_1046 sample_104 sample_1057 sample_106 sample_107 1 1 1 1 1 1 sample_1098 sample_109 sample_1109 sample_1129 sample_1130 sample_1140 1 1 1 1 1 1 sample_1149 sample_115 sample_118 sample_1220 sample_1223 sample_1225 1 1 1 1 1 1
hopefully helps someone.
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