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Revision as of 07:50, 12 March 2010 (view source) Igchoi (Talk | contribs) (→MDS) ← Older edit		Revision as of 07:52, 12 March 2010 (view source) Igchoi (Talk | contribs) (→MDS) Newer edit →
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	#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
	*MDS results		*MDS results
-	#from Exact distance matrix: [[image:mds1.png]]	+	#from Exact distance matrix:<br>[[image:mds1.png]]
-	#from distance matrix cutting off at 99% of the maximum distance: [[image:mds99.png]]	+	#from distance matrix cutting off at 99% of the maximum distance:<br>[[image:mds99.png]]
-	#from distance matrix cutting off at 98% of the maximum distance: [[image:mds98.png]]	+	#from distance matrix cutting off at 98% of the maximum distance:<br>[[image:mds98.png]]
-	#from distance matrix cutting off at 97% of the maximum distance: [[image:mds97.png]]	+	#from distance matrix cutting off at 97% of the maximum distance:<br>[[image:mds97.png]]
	==R script sources==		==R script sources==

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Revision as of 07:52, 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

• MDS results

1. from Exact distance matrix:
   
2. from distance matrix cutting off at 99% of the maximum distance:
   
3. from distance matrix cutting off at 98% of the maximum distance:
   
4. from distance matrix cutting off at 97% of the maximum distance:
   

R script sources