# Tagged Questions

24 views

### Cluster migration visualization

I have asked a very similar question at the Latex forum here, but in order to address the part of my question where I ask if there is a better way of visualizing the data I have, I wanted to cross ...
41 views

### Good (2d) visualization of a mixture model clustering

I have a specific problem which I'm surprised I don't find answers on-line and I hope somebody here has a good suggestion for me. I'm working with a large data set which I'm clustering into specific ...
115 views

### How can I cluster data in a grid-like fashion and heat map the averages in R?

I have a data frame of 3 columns. The first one is the response variable the second and the third ones are some criteria. You can create your own example similar to mine, using this piece of code with ...
259 views

### How to plot Optics Clustering result in Matlab (reachability plot)

I modified the following script for Optics clustering ( http://chemometria.us.edu.pl/download/OPTICS.M ) in order to work with DTW distance instead than Euclidean's. I obtained the Order vector ...
76 views

### Interpretation of NbClust result

The plots show the output of NbClust(). By looking at the plot, is that correct to say that k=5 is the optimal number of ...
46 views

### How do multi-attribute edge-weights influence community detection?

My graph consists of a computer network topology where each vertex is a physical node/device (depicted using its IP address). Two vertices will have an edge if the nodes have had communication with ...
121 views

### Hierarchical clustering of correlation matrix

I have a correlation matrix of 8,854 * 8,854 size. These are Pearson correlation coefficient values in the matrix. I want to perform Hierarchical clustering and create good resolution images like I ...
63 views

### Finding clusters to fit least squares and produce a piecewise equation

In the figure below, I've manually drawn an approximate solution to a least squares fit of the associated regions separated by black lines. The data appears to be bounded by two asymptotes (y=-18 and ...
311 views

### Multidimensional scaling using Python

I have 6,000 points for which I have all pairwise distances in a distance matrix. I want to get an idea whether these data were generated by a mixture of Gaussian distributions so I'm trying to get a ...
309 views

### Interpret clustering plotted in the first two principal components

I got this plot when I plotted a clustering object in R. If I run km <- clara(data, 2), then plot(km), I get a similar ...
150 views

### Which analysis for a set of (0/1)binary variables alone?

I have a dataset I would like to analyze and plot It consists of 100 binary variables (0/1) for about 2,000,000 observations There is absolutely no quantitative variable, nor anything I could use as ...
244 views

### Does Newman's network modularity work for signed, weighted graphs?

The modularity of a graph is defined on its Wikipedia page. In a different post, somebody explained that modularity can easily be computed (and maximized) for weighted networks because the adjacency ...
1k views

### Clustering with Weka

I have to analyse a data set with weka clustering, using 3 clustering algorithms and I need to provide a comparison between them about their performance and suitability. The comparison may include a ...
39 views

### What is exactly code vector and quantization vector of self organizing map?

I am trying to understand code vector in self organizing map. Could anybody explain me intuitively what it is exactly?
42 views

### Clustering data for occurrence

I have a set of data representing nodes and how often they have been involved with each other. I've processed this into a table containing the nodes on X and Y with the data being the number of ...
119 views

### Neighborhood analysis in Matlab using a dot plot

I have points in a 2D graph (coordinates: X,Y property: Z). I would like to find for every point the closest, for example, 5 points and save their properties. What would be the easiest approach? ...
415 views

### Interpretation of PCA biplot?

I just ran my first ever PCA, so please excuse any naivety on my part. As input, I used five years worth of the following: S&P/ASX 200 A-REIT S&P/ASX 200 Consumer Discretionary S&P/ASX ...
44 views

### Weighing probabilities into a polygon

I have a collection of 4-member probability vectors (essentially proportions over 4 mutually exclusive categories). Is there a method to represent this data as a cloud of points inside a square? If ...
2k views

### K-Means Clustering - Calculating Euclidean distances in a multiple variable dataset

I have just completed a simple exercise with 2 variables (X and Y) to understand how K-Means clustering works. The results look like this, My questions is, if I have another column Z, how should ...
146 views

### How to properly color clusters for visualization

I've some data that I can express as an image. Within this data I found some clusters (shown in the image below). I can just assign different colors to different clusters and visualize the image but ...
89 views

### Cluster centroids visualization

I've some data that I've clustered and calculate the similitude within my cluster centroids to spot which class centroids are close to which ones. My goal was to visualize this as a map of points. I ...
61 views

### Clustering cloud fitting inverse functions

I have a cloud of points that can be clustered so that each set of points in the cluster can be fitted with an inverse function : $f(x) = cte / x$. What would be an approach for clustering my dataset ...
97 views

### Three-dimensional phylogenetic tree “anchored” in a scatter plot

I have done a simple clustering (protoclust) using error-containing data. To determine distances, I used a simple "pseudo-d" distance, in which the absolute value of the difference between two points ...
435 views

### Sorting/Clustering similarity matrices

I wonder, what are the available libraries in R or Python to do correlation matrix clustering (sometimes it is referred to clustering). I also, wonder, after clustering/grouping each point. What is ...
809 views

### Interpreting Cluster Heat Maps From R

So I have been looking at how to plot high dimensional clustered data, and one of the options that come up is a heat map. Although there are many webpages that provides code on how to create one, ...
515 views

### Visually plotting multi dimensional cluster data

I have a data set with 16 variables, and after clustering by kmeans, I wish to plot the two groups. What plots do you suggest to visually represent the two clusters?
221 views

### Rounding when making a histogram

Suppose that when making a histogram, one encounters a datum at a bin boundary. Is there a convention on how to round it? For example, suppose my data are integer percentages, running from 0% to ...
998 views

### R: Visualizing document clustering results

I have a k-means clustering result with 35 clusters, there are 5000 documents that each belong to one of the 35 cluster. I would like to visualize the results of the clustering algorithm on a scatter ...
329 views

### Index plot for each cluster sorted by the silhouette

After a cluster analysis IÂ´m trying to plot for each cluster the Index plot of the Silhouette value instead of for the complete dataset (like in the WeightedCluster Library Manual by Matthias ...
212 views

### Clusters produced by R intersect

I am new here - and relatively new to statistics, data mining and R. I am trying to understand why my data is not clustering correctly - or if I am reading it wrong. Shortly about the project: My ...
369 views

### Evaluating clusters of first-order Markov chains

I clustered my dataset of several thousand first-order Markov chains into about 10 clusters. Is there some recommended way how I can evaluate these clusters and find out what the items in the ...
763 views

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637 views

### Appropriateness of PCA to visualize clusters in genetic data

I've seen PCA improperly applied in genetic research quite often. I wanted to clarify : when is it appropriate to use PCA as a visualization tool in your analysis? Some examples: 1) Rarely is the % ...
70 views

### Plotting decay in clustering?

I've got a method that produces clusters of elements and singletons. The singletons usually comprise about half of the initial element set, and there usually is a single biggest cluster of a several ...
1k views

### Looking for 2D artificial data to demonstrate properties of clustering algorithms

I am looking for datasets of 2 dimensional datapoints (each datapoint is a vector of two values (x,y)) following different distributions and forms. Code to generate such data would also be helpful. I ...
78 views

### R: looking for “time” clusters in a data set

I am new to R and seeking some advice. I have a set (~20M) of data describing on which step a process did fail or succeeded: ...
1k views

### How to plot results from text mining (e.g. classification or clustering)?

In text classification and clustering, the number of features are normally big, e.g. I currently get are around 5,000 features which is already really small compared to many other text mining tasks. ...
352 views

### Cluster similarity percentages with inverted Y-axis in R

I'd like to ask a question here that I've also asked on Biostar (stackexchange) and someone there forwarded me to this website. I was wondering how I could perform a Bray Curtis similarity clustering ...
486 views

### Dimensionality reduction technique to maximize separation of known clusters?

So let's say I have a bunch of data points in R^n, where n is pretty big (like, 50). I know this data falls into 3 clusters, and I know which cluster each data point is a part of. All I want to do is ...
1k views

### Visualizing multi-dimensional data (LSI) in 2D

I'm using latent semantic indexing to find similarities between documents (thanks, JMS!) After dimension reduction, I've tried k-means clustering to group the documents into clusters, which works ...
6k views

### How to interpret mean of Silhouette plot?

Im trying to use silhouette plot to determine the number of cluster in my dataset. Given the dataset Train , i used the following matlab code ...
3k views

### How to plot data output of clustering?

I tried clustering a set of data (a set of marks) and got 2 clusters. I would like to graphically represent it. Bit confused about the representation, since I don't have the (x,y) coordinates. Also ...
680 views

### How to generate user-friendly summaries of cluster analysis?

I used BIRCH and HAC to do clustering on my data. I want to now what type of information I can include in reports that my users can generate to get more insights on the clusters. I would have to dumb ...
3k views

### Plotting a heatmap given a dendrogram and a distance matrix in R

I have dendrogram and a distance matrix. I wish to compute a heatmap -- without re-doing the distance matrix and clustering. Is there a function in R that permits this?
1k views

### Interpreting output of igraph's fastgreedy.community clustering method

With the help of several people in this community I have been wetting my feet in clustering some social network data using igraph's implementation of modularity-based clustering. I am having some ...
7k views

### How to do community detection in a weighted social network/graph?

I'm wondering if someone could suggest what are good starting points when it comes to performing community detection/graph partitioning/clustering on a graph that has weighted, undirected edges. The ...