Pan-genome
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#do MDS ([[w:multidimensional scaling|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: [[image:mds1.png | + | *MDS results |
+ | #from Exact distance matrix: [[image:mds1.png]] | ||
+ | #from distance matrix cutting off at 99% of the maximum distance: [[image:mds99.png]] | ||
+ | #from distance matrix cutting off at 98% of the maximum distance: [[image:mds98.png]] | ||
+ | #from distance matrix cutting off at 97% of the maximum distance: [[image:mds97.png]] | ||
==R script sources== | ==R script sources== |
Revision as of 07:50, 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
- MDS results
- from Exact distance matrix:
- from distance matrix cutting off at 99% of the maximum distance:
- from distance matrix cutting off at 98% of the maximum distance:
- from distance matrix cutting off at 97% of the maximum distance: