rplothierarchical-clusteringdendrogram
How to line (cut) a dendrogram at the best K
How do I draw a line in a dendrogram that corresponds the best K for a given criteria?
Like this:
Lets suppose that this is my dendrogram, and the best K is 4.
data("mtcars")
myDend <- as.dendrogram(hclust(dist(mtcars)))
plot(myDend)
I know that abline function is able to draw lines in graphs similarly to the one showed above. However, I don't know how could I calculate the height, so the function is used as abline(h = myHeight)
Solution
The information that you need to get the heights came with hclust. It has a variable containing the heights. To get the 4 clusters, you want to draw your line between the 3rd biggest and 4th biggest height.
HC = hclust(dist(mtcars))
myDend <- as.dendrogram(HC)
par(mar=c(7.5,4,2,2))
plot(myDend)
k = 4
n = nrow(mtcars)
MidPoint = (HC$height[n-k] + HC$height[n-k+1]) / 2
abline(h = MidPoint, lty=2)
- How to add a hover-over tooltip to rhandonstable header cell?
- How to detect the right encoding for read.csv?
- Rcpp Rf_warningcall compiler warnings
- Modify the name of factor variables in lm function(summary function)
- Extreme value analysis and quantile estimation using log Pearson type 3 (Pearson III) distribution - R vs Python
- How to hide NAs when using xlsx::saveWorkbook?
- How do I retrieve a simple numeric value from a named numeric vector in R?
- Adding an image in navbar and adjusting alignment in Rmarkdown
- Matching pair-wise columns from left to right across rows in one dataframe to another dataframe and adding new columns with matching values
- Income to outcome flow chart in Sankey plotly R
- color mapping in geom_conn_bundle not showing correctly
- Print R package startup message AFTER automatic package conflict messages instead of before
- Summing a set of R dataframe rows (column-wise), while retaining the first n columns
- Added variable / partial regression plots for groups in an interaction?
- how to make a topoplot in R with coordinates variable distribution
- List of all functions in base R?
- Plotting multiple plots for different initial conditions in one graph
- Printing repetitively on the same line in R
- Generating UI/Server based on initial selection
- Subset dataframe based on pickerInput
- How to let user pick the data in R-shiny?
- Couldn't show my simple bar charts separately on Shiny R dashboardBody
- How to programmatically filter contents of a second shiny app displayed via iframe
- How to select specific interesting groups for the boxplot in R Shiny app?
- Crosstable and Plot grouping with reactive values
- Is there a way to make multiple Shiny picker inputs where the selections must be disjoint?
- Delay/avoid duplication of shiny server side functions until after credentials
- Predictions only returns value "1"
- How to display a busy indicator in a shiny app?
- Append doesn't work when writing to CSV in R