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Revision as of 07:47, 12 March 2010 (view source) Igchoi (Talk | contribs) (→MDS) ← Older edit		Revision as of 07:48, 12 March 2010 (view source) Igchoi (Talk | contribs) (→MDS) Newer edit →
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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 exact distance matrix]]	+	*Exact distance matrix: [[image:mds1.png|thumb|MDS exact distance matrix]]
	==R script sources==		==R script sources==

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Revision as of 07:48, 12 March 2010

Contents 1 Pan-Genomic Universe 1.1 Data 1.2 Results 1.2.1 MDS 1.3 R script sources

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

1. build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - euclidean distance
2. do MDS (multidimensional scaling) of the distance matrix
3. get coordinates from the first three dimension and plot them in a 3D-space

• Exact distance matrix:
  

  

  MDS exact distance matrix

R script sources