Pan-genome
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*Procedures | *Procedures | ||
#build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - [[w:Euclidean distance|euclidean distance]] | #build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - [[w:Euclidean distance|euclidean distance]] | ||
| - | #do MDS (multidimensional scaling) of the distance matrix | + | #do MDS ([[w:multidimensional scaling|multidimensional scaling]]) of the distance matrix |
#get coordinates from the first three dimension and plot them in a 3D-space | #get coordinates from the first three dimension and plot them in a 3D-space | ||
*Exact distance matrix | *Exact distance matrix | ||
==R script sources== | ==R script sources== | ||
Revision as of 07:45, 12 March 2010
Contents |
Pan-Genomic Universe
Data
- Pan-Genome data version 0.1 Feb 2010
- Download the frequency profile (1,137 genomes x 11,912 pfam domains)
- download: The FP(Frequency Profile) matrix
Results
MDS
- Procedures
- build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - euclidean distance
- do MDS (multidimensional scaling) of the distance matrix
- get coordinates from the first three dimension and plot them in a 3D-space
- Exact distance matrix
