Plotting Minimum Distance within clusters and linkage distance between clusters - r

Question

I using Hierarchical average-linkage method to do clustering using Euclidean distance. To find cluster number (k) to cut I need to do two plots one for Minimum Distance within clusters against number of cluster (graph 1) and one for linkage distance between clusters against number of cluster (graph 2).
> df
Site1 Site2 Site3 Site4 Site5 Site6
1985 11 0 5 15 13 15
1986 12 12 5 31 14 26
1987 23 21 17 14 25 12
1988 22 25 18 17 24 14
1989 11 16 8 18 13 19
1990 7 5 21 8 9 24
1991 20 13 9 21 22 7
1992 15 11 6 19 17 20
1993 19 18 9 11 21 11
1994 33 9 28 17 26 20
1995 16 14 19 33 17 10
1996 14 21 25 4 6 47
1997 4 0 11 22 14 16
1998 10 31 13 26 12 14
1999 24 17 18 41 19 20
2000 21 17 23 19 23 14
2001 12 8 6 7 19 20
2002 19 24 19 31 24 17
2003 13 29 10 28 7 9
2004 19 14 19 22 20 13
2005 16 8 9 10 11 13
2006 8 9 46 9 20 19
2007 12 10 15 13 10 9
2008 12 18 25 12 47 22
2009 19 18 18 23 21 20
2010 23 10 46 35 25 12
2011 20 35 18 30 22 18
2012 23 13 23 34 25 34
2013 17 28 20 13 19 21
2014 19 22 16 16 21 23
df2 <- data.frame(t(df))
tree <- hclust(dist(df2))

Answer 1

Since there's no question stated, I'm assuming that you are interested to plot the figure above with the example data-set. Please correct if I'm wrong with that assumption.
(i) find the number of groups based on sequence linkage distances. Sequence of linkage distance in this case was eyeballed from plot(tree):
library(dplyr)
cls.df <- data.frame(h=40:100)
cls.df$k <- sapply(cls.df$h, function(x) cutree(tree, h=x) %>% max )
(ii) clean the table by retaining only the minimum linkages distance h for number of group k
cls.df <- cls.df %>%
group_by(k) %>%
summarise(h=min(h))
(iii) Plot:
library(ggplot2)
ggplot(cls.df, aes(k, h)) +
geom_line() +
geom_point() +
theme_bw() +
ylab("Linkage Distance") +
xlab("Number of Cluster")