markov_clustering
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GuyAllard
markov clustering in python
Traceback: ``` Traceback (most recent call last): File "cluster_network.py", line 19, in result = mc.run_mcl(matrix, inflation=inflation) File "/home/itan_lab/david/.conda/envs/goflof/lib/python3.7/site-packages/markov_clustering/mcl.py", line 228, in run_mcl matrix = iterate(matrix, expansion, inflation) File "/home/itan_lab/david/.conda/envs/goflof/lib/python3.7/site-packages/markov_clustering/mcl.py", line...
Hello, I am trying to use draw_graph but there is an error that: module 'markov_clustering' has no attribute 'draw_graph'. The same is working in google colab but not in jupyter...
Just tried to run the example code given on github readme. import markov_clustering as mc ``` import networkx as nx import random # number of nodes to use numnodes =...
``` result = mc.run_mcl(score, **kwargs) clusters = mc.get_clusters(result) modularity = mc.modularity(matrix=result, clusters=clusters) ``` as score is a np.ndarray (np.matrix is depreciated and data is not sparse) result is also a...
Hi I have 2 questions. 1) In the example using the modularity only the inflation is varied. When would we vary the expansion. Is there a case where we would...
In calculating modularity Q I get the following error in my script that uses the markov_clustering package: ``` Traceback (most recent call last): File "mcl_3_inflat_test.py", line 48, in Q =...
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) in ----> 1 result = mc.run_mcl(matrix) # run MCL with default parameters 2 clusters = mc.get_clusters(result) # get clusters ~\Anaconda3\lib\site-packages\markov_clustering\mcl.py in run_mcl(matrix, expansion,...
Hi, I am using it to identify clusters of cytology cells. I have feature set for around 50K cells which I can use to find clusters using the example provided....
The example given includes 200 nodes and 2D coordinates. I am new to Markov Clustering. I can get sequence-sequence similarity from blast for each gene pair, for example, my current...
