[R] Igraph library: How to calculate APSP (shortest path matrix) matrix for a subset list of nodes.

Dear R Users, I have a network of 25000 total nodes and a list of 500 node which is a subset of all nodes. Now I want to calculate the APSP (all pair shortest path) matrix only for these 500 nodes. I would appreciate any help. Thanks in advance Dinesh -- Dinesh Kumar Barupal Research Associate

[R] Subset of matrix

145742 1123 I would appreciate if you can use this matrix as input. Thanks in advance. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu

[R] Alignment and Reshaping of the matrix

Where first column represent the Variable name. And if the first matrix is transposed, then how to get the output in which First raw present the variable name. It will be great help for my research. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451

[R] Two Colored Heatmap

NoUp Down No TrehaloseNo UpUp Down Up First raw and first column are labels. Each column present a condition. I want to create a heatmap which colored UP = RED, Down= Blue and No= White. Thanks in Advance. Dinesh -- Dinesh Kumar Barupal Research

[R] For Subset or Reshaping the Table

matrix in this format Row Col Value a D 4 a E 5 a F 6 .. .. e E 9 I want only the pair which pass a threshold for example >3. Please help me. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center

[R] Reshape a matrix

Dear R users, I have a matrix like A X1 B Y2 C Z3 I want to reshape this matrix into this format X Y Z A 1 B 2 C 3 Thanks in advance for your help. Dinesh -- Dinesh Kumar Barupal Junior Specialist Metabolomics Fiehn Lab

[R] similarity matrix to dendrogram (GML format)

Dear R users I have a similarity matrix of 100X100 (chemical similarity). Now I want to create a dendrogram from it and export this dendrogram as GML format network. Can you please reply How I can do this stuff? Thanks in advance. Dinesh -- Dinesh Kumar Barupal Junior Specialist Metabolomics