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Re: [igraph] Using iGraph for correlated abundances

From: Gábor Csárdi
Subject: Re: [igraph] Using iGraph for correlated abundances
Date: Tue, 12 Aug 2014 10:53:59 -0400

Hi Tim,

yes, you can delete any edges from an you want from an igraph object
with delete.edges.

Maybe you want to set some elements of a matrix zero, then do it like this:

M[ condition ] <- 0

E.g. if you have pairwise p values in another matrix, then you can say:

M [ p > p_threshold ] <- 0

To say something more specific, you need to tell us more precisely
what you are doing. E.g. see
for advice on how to ask questions about R and R packages.


On Tue, Aug 12, 2014 at 10:37 AM, Tim Richter-Heitmann
<address@hidden> wrote:
> Hi there,
> i have a very basic question. I want to plot my large abundance data
> according to simple pairwise x,y pearson and/or spearman correlation.
> I have used qgraph so far, but it cannot filter for non-significant p-values
> (it can either display significant observations or correlation strengths,
> but not both).
> My question is, can iGraph do that by omitting non significant values at
> all?
> I just recently delved into network analysis, from what ive seen on the net,
> the graph.adjacency is the most common way to do so, and ive seen examples
> for
> deleting edges not meeting tresholds, but ive not seen the significancy
> covered yet.
> Also fine would be coloring according to cor-strength, label width according
> to significancy level (or vice versa).
> Any example code is very welcome. Thank you very much!
> Tim
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