I am trying to see how some known labels explain, or are adjusted to the 2D representation from my data that I get from UMAP.
I tried to use silhouette
function but the cluster information must be provided as a numeric vector and then these are the one that plot(sil)
shows. Is there a way to use the cluster names or at least show these in the plot instead of the numbers?
(similar question as here but instead of the sample labels I want to change the cluster labels)
For example:
# run hierarchical clustering
if(!require("cluster")) { install.packages("cluster"); require("cluster") }
tmp <- matrix(c( 0, 20, 20, 20, 40, 60, 60, 60, 100, 120, 120, 120,
20, 0, 30, 50, 60, 80, 40, 80, 120, 100, 140, 120,
20, 30, 0, 40, 60, 80, 80, 80, 120, 140, 140, 80,
20, 50, 40, 0, 60, 80, 80, 80, 120, 140, 140, 140,
40, 60, 60, 60, 0, 20, 20, 20, 60, 80, 80, 80,
60, 80, 80, 80, 20, 0, 20, 20, 40, 60, 60, 60,
60, 40, 80, 80, 20, 20, 0, 20, 60, 80, 80, 80,
60, 80, 80, 80, 20, 20, 20, 0, 60, 80, 80, 80,
100, 120, 120, 120, 60, 40, 60, 60, 0, 20, 20, 20,
120, 100, 140, 140, 80, 60, 80, 80, 20, 0, 20, 20,
120, 140, 140, 140, 80, 60, 80, 80, 20, 20, 0, 20,
120, 120, 80, 140, 80, 60, 80, 80, 20, 20, 20, 0),
nr=12, dimnames=list(LETTERS[1:12], LETTERS[1:12]))
cl <- hclust(as.dist(tmp,diag = TRUE, upper = TRUE), method= 'single')
cluster_labels<-cutree(cl, h=25)
#here I would like to change the cluster labels from numbers to letters, for example:
#cluster_labels<-LETTERS[1:length(unique(cluster_labels))][cluster_labels]
sil_cl <- silhouette( cluster_labels,as.dist(tmp), title=title(main = 'Good'))
plot(sil_cl)#the plot should show the cluster labels instead of the numbers
I figured out this can be done using factoextra
package. But it would be nice if anyone finds the way to do it with the regular plot()
function though
if(!require("cluster")) { install.packages("cluster"); require("cluster") }
if(!require("factoextra")) { install.packages("factoextra"); require("factoextra") }
tmp <- matrix(c( 0, 20, 20, 20, 40, 60, 60, 60, 100, 120, 120, 120,
20, 0, 30, 50, 60, 80, 40, 80, 120, 100, 140, 120,
20, 30, 0, 40, 60, 80, 80, 80, 120, 140, 140, 80,
20, 50, 40, 0, 60, 80, 80, 80, 120, 140, 140, 140,
40, 60, 60, 60, 0, 20, 20, 20, 60, 80, 80, 80,
60, 80, 80, 80, 20, 0, 20, 20, 40, 60, 60, 60,
60, 40, 80, 80, 20, 20, 0, 20, 60, 80, 80, 80,
60, 80, 80, 80, 20, 20, 20, 0, 60, 80, 80, 80,
100, 120, 120, 120, 60, 40, 60, 60, 0, 20, 20, 20,
120, 100, 140, 140, 80, 60, 80, 80, 20, 0, 20, 20,
120, 140, 140, 140, 80, 60, 80, 80, 20, 20, 0, 20,
120, 120, 80, 140, 80, 60, 80, 80, 20, 20, 20, 0),
nr=12, dimnames=list(LETTERS[1:12], LETTERS[1:12]))
cl <- hclust(as.dist(tmp,diag = TRUE, upper = TRUE), method= 'single')
cluster_labels<-cutree(cl, h=25)
sil_cl <- silhouette( cluster_labels,as.dist(tmp), title=title(main = 'Good'))
fviz_silhouette(sil_cl)+scale_fill_discrete(labels=LETTERS[1:12])+guides(col=FALSE)