I searched this forum and found many related questions about network. I will try to be as precise as necessary.
Suppose I get a partial correlation (PC) matrix (from RNA-seq) and want to use the PC matrix to build my gene-gene interaction (GGI) network. The edges can be pruned/trimmed by a threshold PC value. Now I want to
Visualize the vertices and edges
Display + and - PC values differently (e.g. red for + & blue for -)
Visualize the magnitude of the PC (e.g. a thicker line for a bigger PC and a thinner line for a smaller PC)
Ideally a R package, but a java or perl package or anything that runs on a ubuntu machine would work
BTW, is there a good software product that can generate directional graph (interactions with directions)? I know a set of time series data would be needed to generate a directional graph. Time series is often not satisfied, but I guess in general a set of samples treated with increasing concentrations of a compound with the same length of time might simulate a time series.
Thanks in advance!