[R] Questions about 'igraph' package.......

karena dr.jzhou at gmail.com
Mon Mar 28 21:05:09 CEST 2011


I am using 'igraph' package to make some graphs of 'gene-gene interaction'.

I can get a data.frame which has three columns.
gene1      gene2          pvalue
AGT         MLR            1.2e-04
MLR         11BHSD1      1.71e-05
IFG2        11BHSD2      2.2e-07
.             .                 .
.             .                 .
.             .                 .
AGTR1     NPPA            3.2e-2

I have several questions:
1) How can I make a plot in which the width of the edges can represent the
significance of the epistasis p values? I am thinking about getting another
column which is the -log(pvalue), so the larger the value is the more
significant the p value is. 

2) After I get the graph, how can I modify the image. Because all the nodes
in the image are numbers (0,1,.....,100), how can I add the gene name to
each node in the image?
 

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