deeenes

Cambridge, United Kingdom

ebi.ac.uk/~denes

I am a biologist, doing bioinformatics, working with networks of signaling pathways, using primarily python with igraph. Sometimes I code in R, PHP, javascript and bash. I love MySQL, especially 100+ lines long queries. I use LaTeX often, with beamer and TikZ, I love typography and graphic design.

Jan
25
comment igraph invalid vertex Id
It depends on your data if it makes sense to take the average/minimum/maximum weight of 2 edges of the opposite directections, and then run fastgreedy. I can imagine it does not make sense at all, and then you should not use fastgreedy, but only other methods.
Jan
25
comment igraph invalid vertex Id
If you build a graph with directed = True, then you can add 1 -> 2 and/or 2 -> 1 edge separately. If you build an undirected graph, it does not matter if you add 1 -> 2 or 2 -> 1, the two endpoints are equal, and it is only matter of chance which will be the "source" or "target", because undirected edges don't have source and target, just 2 endpoints, it is really random. You should not assume in case of undirected graph that source will be 1 if you added the edge 1 -> 2, because it can be 2 with equal chance. That's why it is undirected.
Jan
25
comment igraph invalid vertex Id
You can not run fastgreedy on undirected graph, igraph simply throws an error if you try.
Jan
24
awarded Scholar
Jan
24
accepted How to visit an institute when looking for job?
Jan
23
revised igraph invalid vertex Id
adding info about igraph's reindexing
Jan
23
revised igraph invalid vertex Id
adding info about directed/undirected graphs
Jan
23
comment igraph invalid vertex Id
You can still use fastgreedy, but it does not consider directionality, so you loose that additional information. Once you initialize the igraph.Graph() object, you decide if it will be a directed or undirected network. Here we initialized it to be undirected, exactly because fastgreedy needs an undirected graph. If you use other methods, like spinglass, which are able to consider directions, you should create a directed network: igraph.Graph.TupleList(L, directed = True, ...). You can also convert between directed and undirected graphs with as_directed() and as_undirected() methods.
Jan
23
answered igraph invalid vertex Id
Jan
19
awarded Supporter
Jan
17
awarded Yearling
Jan
16
awarded Yearling
Jan
11
comment Coordinates of box of annotations in matplotlib
For me neither fig.canvas.draw() or plt.draw() resolved the "RuntimeError: Cannot get window extent w/o renderer" error, but only fig.savefig('something.pdf'). After doing the following work, I save it again.
Jan
3
comment How to add "irrelevant" edges
to avoid even this small change, one could add all the edges even in the first version, but with style=invis for the dashed edges, so those won't be visible
Dec
3
comment Similarity measure for short series
thanks @spdrnl, now I am considering euclidean distance too. I decided to try all of them, and see which gives the best sensitivity/specificity compared to a gold standard.
Dec
2
asked Similarity measure for short series
Nov
19
comment Compiling Python to C using Cython
for me this answer resulted in compilation of a working extension. answer of RoeeK resolved the linking problem, but after Python failed to import with error ImportError: dynamic module does not define init function. thank you really much, I think would be nicer to write it with less lecturing style without assuming stupidity as the 3 rtfm suggests.
Nov
10
awarded Supporter
Nov
10
awarded Autobiographer
Nov
6
comment How mass spec formate and acetate adducts masses are calculated?
And if anybody else needs the monisotopic masses, here is a nice table: ciaaw.org/atomic-masses.htm
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