I have run a nearest neighbor clustering of some data, and I have a matrix of cosine distances. However, I'm confused on how to plot it visually, or what units, if any these distances exist in.
It seems if I create a scatter plot of the distances, I get a perfectly straight diagonal line. If I flip one axis, things look different, but I'm not sure if that's all there is to it. I have found many of such scatter plots online, but no documentation on the construction of the graphs.
I know that half of the similarity matrix is redundant, so I probably have more data than I need. Personally, that makes things more confusing.
This picture is for reference only. The distances/clustering appear to be slightly different than my model's, but the concept is the same -- it is a scatter plot of distances, and I'm just not sure how to know if I set up the X + Y axes correctly.
I have been struggling to provide a good reference graph to give everyone some visual context about what kind of graph / approach I'm interested in. This is the best I have found so far, it's fairly rudimentary, so it may not be 100% cutting edge or fool proof. And you may also notice the axes on those graphs are not labeled, so that makes it hard to conceptualize, at least for me.
There might be better ways to plot document clusters, but this graph will be fine as a reference.
For clarity, my exact data are as follows: I have a tabular structure of parsed text that I transformed into TF-IDF. I ran a nearest neighbor clustering algorithm on it, and I have a similarity matrix resulting from that. My goal is to plot the documents on a graph, based on how the clustering algorithm grouped them based on the TF-IDF nearest neighbors. In other words, assigning a color to each cluster. The color part seems easy enough, but I'm just not sure what the axes are, or what space my documents 'exist' in, making it hard to conceptualize how to plot them. If you have any other questions about what I'm trying to do, I'd be happy to articulate further.