Re: [igraph] Using iGraph for correlated abundances

[Tim Richter-Heitmann]

Hi again!

Thank you for replying that quickly. You helpfully pointed out i could just 
manipulate my correlation matrix before i carry out my plotting.
That was very helpful on its own.

Currently, as i have just started with network analysis, i use rather 
easy-to-grasp approaches.
iGraph seems to be much more powerful than qGraph, but it seems like i need a 
while to get an idea how to get my graphs out. For example:

qgraph(cor(df, method="spearman", use="pairwise.complete.obs"), layout="spring", 
minimum=0.4, shape="circle",  label.cex=0.4, vsize=0.4
, groups=list, legend=TRUE, border.width=0.1, color=c25, filetype="pdf", 
filename="1", height=80, width=80, legend.cex=5, usePCH=TRUE)

gives me a non-circular, spring-outlaid network of spearman rank correlation 
from my input dataframe, in which i could control node sizes/shapes, could 
colourize by a vector with group IDs according to my own palette,
and which ignored correlations not meeting my treshold of 0.4.
I need now to translate this into iGraph, which seems very untrivial to do, for 
example, i have yet to find out how to control graphical parameters with 
graph.adjacency.
But i hope i can get back to you later once i developed some expertise with 
iGraph. Thanks again!

Tim


 Message: 2
Date: Tue, 12 Aug 2014 10:53:59 -0400
From: G?bor Cs?rdi<address@hidden>
To: Help for igraph users<address@hidden>
Subject: Re: [igraph] Using iGraph for correlated abundances
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset=UTF-8

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
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
for advice on how to ask questions about R and R packages.

Gabor

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
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> https://lists.nongnu.org/mailman/listinfo/igraph-help


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End of igraph-help Digest, Vol 97, Issue 5
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--
Tim Richter-Heitmann (M.Sc.)
PhD Candidate



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