Category: Dendrogram networkx

Dendrogram networkx

dendrogram networkx

There are a lot of clustering algorithms to choose from. The standard sklearn clustering suite has thirteen different clustering classes alone. So what clustering algorithms should you be using? As with every question in data science and machine learning it depends on your data.

A number of those thirteen classes in sklearn are specialised for certain tasks such as co-clustering and bi-clustering, or clustering features instead data points. Obviously an algorithm specializing in text clustering is going to be the right choice for clustering text data, and other algorithms specialize in other specific kinds of data.

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Thus, if you know enough about your data, you can narrow down on the clustering algorithm that best suits that kind of data, or the sorts of important properties your data has, or the sorts of clustering you need done. So, what algorithm is good for exploratory data analysis? There are other nice to have features like soft clusters, or overlapping clusters, but the above desiderata is enough to get started with because, oddly enough, very few clustering algorithms can satisfy them all!

Next we need some data. So, on to testing ….

Dendrograms in Python

Before we try doing the clustering, there are some things to keep in mind as we look at the results. K-Means has a few problems however. That leads to the second problem: you need to specify exactly how many clusters you expect. If you know a lot about your data then that is something you might expect to know.

Finally K-Means is also dependent upon initialization; give it multiple different random starts and you can get multiple different clusterings. This does not engender much confidence in any individual clustering that may result. K-Means scores very poorly on this point.

Best to have many runs and check though. There are few algorithms that can compete with K-Means for performance. If you have truly huge data then K-Means might be your only option. But enough opinion, how does K-Means perform on our test dataset? We see some interesting results. First, the assumption of perfectly globular clusters means that the natural clusters have been spliced and clumped into various more globular shapes. Worse, the noise points get lumped into clusters as well: in some cases, due to where relative cluster centers ended up, points very distant from a cluster get lumped in.The dendrogram illustrates how each cluster is composed by drawing a U-shaped link between a non-singleton cluster and its children.

The top of the U-link indicates a cluster merge.

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The two legs of the U-link indicate which clusters were merged. The length of the two legs of the U-link represents the distance between the child clusters. It is also the cophenetic distance between original observations in the two children clusters.

The linkage matrix encoding the hierarchical clustering to render as a dendrogram. See the linkage function for more information on the format of Z. The dendrogram can be hard to read when the original observation matrix from which the linkage is derived is large. Truncation is used to condense the dendrogram. There are several modes:. No truncation is performed default. The last p non-singleton clusters formed in the linkage are the only non-leaf nodes in the linkage; they correspond to rows Z[n-pend] in Z.

All other non-singleton clusters are contracted into leaf nodes. No more than p levels of the dendrogram tree are displayed. All links connecting nodes with distances greater than or equal to the threshold are colored blue.

By default labels is None so the index of the original observation is used to label the leaf nodes. When True, the final rendering is not performed. This is useful if only the data structures computed for the rendering are needed or if matplotlib is not available. Specifies the angle in degrees to rotate the leaf labels. When unspecified, the rotation is based on the number of nodes in the dendrogram default is 0. Specifies the font size in points of the leaf labels.

When unspecified, the size based on the number of nodes in the dendrogram. The function is expected to return a string with the label for the leaf.If this is your first time using this code, please install the following packages using pip in the terminal:. Installing the graph drawing engines is a little more complicated. To install Graphviz, one must first install homebrew:.

To install PyGraphviz, we need to direct pip this time using pip3 to where Graphviz is located. To do this, simply paste this snippet into the terminal:. Once these are installed, import them into your environment. TIP: When producing dendrograms of multiple neurons, remember to clear the plotting space to avoid all of your dendrograms being plotted ontop of one another.

To do this, use. For Catmaid neurons, the treenodes most distal i. The neato layout takes all the nodes and finds the lowest energy configuration of where the nodes should be placed.

It does this by placing a 'virtual spring' between each node. The force from this spring is proportional to the geodesic distance between the nodes. Imagine you have a bunch of connected, individual springs. You squeeze the ball of springs and let go. Each spring will continue to exert extend or accept contract a force from another spring until the system reaches an equilibrium state. This is a loose analogy as to how the neato algorithm works. As the force is proportional to the distance between notes, this gives neato diagrams an advantage of being able to respect the distance between nodes, giving a more realistic representation of the neuron than the dot layout, which does not consider distance.

Finding this low energy configuration takes a long time, therefore it is strongly recommended that one downsamples the NOI before running the neato algorithm by a factor of Downsampling a neuron will have a greater effect on the representation by the neato algorithm than when using the dot algorithm This is because the dot algorithm does not consider the distance between nodes when plotting; it only plots the neuron hierarchically from the tip of the dendrites to the soma.

The neato algorithm does consider geodesic distance when plotting, so if one downsamples a neuron i. This results in overestimations and underestimations of the actual distance between certain nodes. Felsenberg et al. Skip to content. Branch: master. Create new file Find file History.

Latest commit Fetching latest commit…. Getting Started These notes detail what is required in order to run the Dendrogram Code. This code was used to generate figures 4D and 4F in: Felsenberg et al. You signed in with another tab or window.

Hierarchical clustering of networks

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As the graph breaks down into pieces, the tightly knit community structure is exposed and the result can be depicted as a dendrogram. In NetworkX the implementation returns an iterator over tuples of sets.

First tuple is the first cut consisting of 2 communities, second tuple is the second cut consisting of 3 communities, etc.

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I've looked at scipy. Following ItamarMushkin I followed mdml's answer with slight modifications and got what I wanted. Then I build Za linkage matrix I input to scipy. I understand there may be some redundant iterations here, I haven't thought about optimization yet. Learn more. Asked 2 months ago. Active 2 months ago.

Viewed times. The Girvan-Newman algorithm for community detection in networks: detects communities by progressively removing edges from the original graph. Giora Simchoni Giora Simchoni 1, 1 1 gold badge 19 19 silver badges 40 40 bronze badges. Does this help? Building another directed graph from the list of tuples, which would be a dendrogram, which I would convert to the matrix needed by dendrogram.

This is also an option, drawing the directed graph with a custom dendrogram layout: stackoverflow.Once you have the basics of clustering sorted you may want to dig a little deeper than just the cluster labels returned to you.

Fortunately, the hdbscan library provides you with the facilities to do this. It can be informative to look at that hierarchy, and potentially make use of the extra information contained therein. Suppose we have a dataset for clustering. We can cluster the data as normal, and visualize the labels with different colors and even the cluster membership strengths as levels of saturation. The question now is what does the cluster hierarchy look like — which clusters are near each other, or could perhaps be merged, and which are far apart.

This merely gives us a CondensedTree object. If we want to visualize the hierarchy we can call the plot method:. We can now see the hierarchy as a dendrogram, the width and color of each branch representing the number of points in the cluster at that level. You can even pass a selection palette to color the selections according to the cluster labeling.

From this, we can see, for example, that the yellow cluster at the center of the plot forms early breaking off from the pale blue and purple clusters and persists for a long time.

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You can also see that the pale blue cluster breaks apart into several subclusters that in turn persist for quite some time — so there is some interesting substructure to the pale blue cluster that is not present, for example, in the dark blue cluster. If this was a simple visual analysis of the condensed tree can tell you a lot more about the structure of your data. This is not all we can do with condensed trees, however.

For larger and more complex datasets the tree itself may be very complex, and it may be desirable to run more interesting analytics over the tree itself. As you can see we get a NetworkX directed graph, which we can then use all the regular NetworkX tools and analytics on.

The graph is richer than the visual plot above may lead you to believe, however:. The graph actually contains nodes for all the points falling out of clusters as well as the clusters themselves. Each node has an associated size attribute and each edge has a weight of the lambda value at which that edge forms. This allows for much more interesting analyses. This is equivalent to the pandas DataFrame but is in pure NumPy and hence has no pandas dependencies if you do not wish to use pandas.

We have still more data at our disposal, however. Again we have an object which we can then query for relevant information. The most basic approach is the plot method, just like the condensed tree. As you can see we gain a lot from condensing the tree in terms of better presenting and summarising the data. There is a lot less to be gained from visual inspection of a plot like this and it only gets worse for larger datasets.

The plot function support most of the same functionality as the dendrogram plotting from scipy. In practice, however, you are more likely to be interested in access the raw data for further analysis. The NumPy and pandas results conform to the single linkage hierarchy format of scipy.For more complete documentation, see the Phylogenetics chapter of the Biopython Tutorial and the Bio. Phylo API pages generated from the source code. The Phylo cookbook page has more examples of how to use this module, and the PhyloXML page describes how to attach graphical cues and additional information to a tree.

This module is included in Biopython 1. The Phylo module has also been successfully tested on Jython 2. Each function accepts either a file name or an open file handle, so data can be also loaded from compressed files, StringIO objects, and so on.

The second argument to each function is the target format. Currently, the following formats are supported:. See the PhyloXML page for more examples of using tree objects.

Incrementally parse each tree in the given file or handle, returning an iterator of Tree objects i. BaseTree Tree class, depending on the file format. Parse and return exactly one tree from the given file or handle. If the file contains zero or multiple trees, a ValueError is raised. This is useful if you know a file contains just one tree, to load that tree object directly rather than through parse and nextand as a safety check to ensure the input file does in fact contain exactly one phylogenetic tree at the top level.

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See examples of this in the unit tests for Phylo in the Biopython source code. Write a sequence of Tree objects to the given file or handle. Passing a single Tree object instead of a list or iterable will also work see, Phylo is friendly.

Given two files or handles and two formats, both supported by Bio. Phyloconvert the first file from the first format to the second format, writing the output to the second file. Within the Phylo module are parsers and writers for specific file formats, conforming to the basic top-level API and sometimes adding additional features.

Datasets: Analysing Using Networkx

See the PhyloXML page for details. NewickIO: A port of the parser in Bio. Trees to support the Newick a. NexusIO: Wrappers around Bio. Nexus to support the Nexus tree format.This is a tutorial on how to use scipy's hierarchical clustering.

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One of the benefits of hierarchical clustering is that you don't need to already know the number of clusters k in your data in advance. Sadly, there doesn't seem to be much documentation on how to actually use scipy's hierarchical clustering to make an informed decision and then retrieve the clusters. The only thing you need to make sure is that you convert your data into a matrix X with n samples and m features, so that X.

Well, sure it was, this is python ;but what does the weird 'ward' mean there and how does this actually work? As the scipy linkage docs tell us, 'ward' is one of the methods that can be used to calculate the distance between newly formed clusters.

I think it's a good default choice, but it never hurts to play around with some other common linkage methods like 'single''complete''average'For example, you should have such a weird feeling with long binary feature vectors e.

As you can see there's a lot of choice here and while python and scipy make it very easy to do the clustering, it's you who has to understand and make these choices. If i find the time, i might give some more practical advice about this, but for now i'd urge you to at least read up on the mentioned linked methods and metrics to make a somewhat informed choice.

Another thing you can and should definitely do is check the Cophenetic Correlation Coefficient of your clustering with help of the cophenet function. This very very briefly compares correlates the actual pairwise distances of all your samples to those implied by the hierarchical clustering.

dendrogram networkx

The closer the value is to 1, the better the clustering preserves the original distances, which in our case is pretty close:. No matter what method and metric you pick, the linkage function will use that method and metric to calculate the distances of the clusters starting with your n individual samples aka data points as singleton clusters and in each iteration will merge the two clusters which have the smallest distance according the selected method and metric.

It will return an array of length n - 1 giving you information about the n - 1 cluster merges which it needs to pairwise merge n clusters.

dendrogram networkx

Z[i] will tell us which clusters were merged in the i -th iteration, let's take a look at the first two points that were merged:. In its first iteration the linkage algorithm decided to merge the two clusters original samples here with indices 52 and 53, as they only had a distance of 0. This created a cluster with a total of 2 samples. In the second iteration the algorithm decided to merge the clusters original samples here as well with indices 14 and 79, which had a distance of 0.

This again formed another cluster with a total of 2 samples. The indices of the clusters until now correspond to our samples. Remember that we had a total of samples, so indices 0 to Let's have a look at the first 20 iterations:.

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