title: Delete weak correlations from network in igraph (vertices and edges)
body: <p>I need to plot a network from a correlation matrix.
  A small subset of my data:</p>
  
  <pre><code>Taxon                                                          CD1         CD2
  Actinomycetaceae;g__Actinomyces                        0.072998825 0.031399459
  Coriobacteriaceae;g__Atopobium                         0.040946468 0.002703265
  Corynebacteriaceae;g__Corynebacterium                  0.002517201 0.006446247
  Micrococcaceae;g__Rothia                               0.001174694 0.002703265
  Porphyromonadaceae;g__Porphyromonas                    0.023326061 0.114368892
  Prevotellaceae;g__Prevotella                           0.252894781 0.102308172
  Flavobacteriaceae;g__Capnocytophaga                    0.001174694 0.029320025
  Aerococcaceae;g__Abiotrophia                           0.002013761 0.003327095
  Carnobacteriaceae;g__Granulicatella                    0.042960228 0.049490539
  Gemellaceae;g__Gemella                                 0.027857023 0.067165731
  Streptococcaceae;g__Streptococcus                      0.220506796 0.182782283
  ClostridialesFamilyXI.IncertaeSedis;g__                0.000000000 0.000623830
  ClostridialesFamilyXIII.IncertaeSedis;g__Mogibacterium 0.006880349 0.002495321
  Lachnospiraceae;Other                                  0.000335627 0.000831774
  Clostridia                                             0.004363148 0.002079434
  Lachnospiraceae;g__Oribacterium                        0.003524081 0.002079434
  Peptostreptococcaceae;g__Peptostreptococcus            0.000167813 0.005198586
  Veillonellaceae;Other                                  0.001342507 0.001455604
  Veillonellaceae;g__Veillonella                         0.047323376 0.082553545
  Fusobacteriaceae;g__Fusobacterium                      0.009229737 0.010813059
  Fusobacteriaceae;g__Leptotrichia                       0.092465179 0.076523186
  Neisseriaceae;g__Neisseria                             0.013592885 0.027656477
  Pasteurellaceae;g__Haemophilus                         0.014431952 0.092534831
  SR1;c__;f__;g__                                        0.000000000 0.002079434
  TM7;c__TM7-3;f__;g__                                   0.065782849 0.018299023
  Erysipelotrichaceae;g__Bulleidia                       0.007551603 0.004366812
  Bacteroidia                                            0.000000000 0.000415887
  Porphyromonadaceae;g__Tannerella                       0.000671254 0.002079434
  Flavobacteriaceae                                      0.002013761 0.001247661
  Bacilli                                                0.002181574 0.002911208
  Clostridia;f__;g__                                     0.000671254 0.002703265
  ClostridialesFamilyXIII.IncertaeSedis;g__Eubacterium   0.003020641 0.002079434
  Lachnospiraceae;g__Moryella                            0.003188454 0.000623830
  Veillonellaceae;g__Selenomonas                         0.004866588 0.021834061
  Fusobacteriaceae                                       0.000335627 0.001871491
  Campylobacteraceae;g__Campylobacter                    0.001510321 0.001247661
  Pasteurellaceae;g__Actinobacillus                      0.002852828 0.000207943
  Burkholderiaceae;g__Lautropia                          0.000000000 0.002495321
  Lactobacillaceae;g__Lactobacillus                      0.000000000 0.000000000
  Staphylococcaceae;g__Staphylococcus                    0.000000000 0.000000000
  </code></pre>
  
  <p>This is what I did:</p>
  
  <pre><code>library(vegan)
  library(psych)
  
  mydata &lt;- read.csv(file="L5_filt.txt", header=T, row.names=1, sep="\t")
  mydata_t &lt;- t(as.matrix(mydata))
  graph.f&lt;-graph.adjacency(cor.matrix$r, weighted=TRUE, mode="upper")
  
  t.names &lt;- colnames(cor.matrix)[as.numeric(V(t.graph)$name)]
  graph.f = simplify(graph.f)
  </code></pre>
  
  <p>I want to plot only strong correlations (>+0.6 and &lt;-0.6)
  I want different colors for edges relative to positive and negative correlations!</p>
  
  <pre><code>E(graph.f)[weight &lt; 0.6 &amp; weight &gt; -0.6]$width&lt;-0
  E(graph.f)[weight &gt; 0.6]$width&lt;-2.5
  E(graph.f)[weight &lt; -0.6]$width&lt;-2.5
  E(graph.f)[weight &gt; 0.6]$color&lt;-"red"
  E(graph.f)[weight &lt; -0.6]$color&lt;-"green"
  
  par(mai=c(1,1,0.1,0.15), mar=c(1, 0, 1, 1), mgp=c(2,1,0), mfrow=c(1,2), cex=0.7, lwd=0.5)
  plot (graph.f, vertex.size=5, vertex.shape="circle", vertex.label.color="red", 
      vertex.label=t.names, vertex.label.cex=0.9, layout=layout.fruchterman.reingold)
  </code></pre>
  
  <p>The result is really near to what I want, but I don't know how to delete from the plot the vertices with weak correlations (I mean the nodes related to the edges for which I set width=0) and the names of these vertices.</p>
  
  <p>How can I modify my code?</p>
  
  <p>Thanks!</p>