[adegenet-forum] sPCA for environmental genomics

[Nicolas.Tsesmetzis at shell.com]

Hello adegenet users,
I am working in environmental genomics looking at microbial communities in environmental samples (mostly soil). As each soil sample can contain thousands of microorganisms (at different relative abundances) we typically use Principal Coordinate Analysis (PCoA) to identify samples that are similar to each other. What would be really useful is if we could include geospatial information (Lat, Long) in the analysis in order to determine whether the similarities in the microbial profiles are due to their geospatial proximity (and the underlying environmental parameters associated with that geographic area).
Searching for such type of analysis I came across the sPCA functionality in the adegenet package. Is sPCA suitable for such analysis? If so, would it be possible to retrofit the sPCA function in adegenet to perform such analysis? If not, could anyone point me to a tool (or a person) that could help me with this type of analysis?
The input table is very simple:


Organism 1

Organism 2

Organism 3

....

 Organism m

Lat

Long

Sample 1

0.5

0.1

0

....

0.2

x1

y1

Sample 2

0.2

0

0

....

0.4

x2

y2

Sample 3

0.1

0.8

0.6

....

0

x3

y3

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

Sample n

0.06

0.1

0



0.2

xn

yn

Total

1

1

1



1





 Thank you all very much in advance for any pointers.
Kind regards,
Nicolas Tsesmetzis, PhD
Shell International Exploration and Production Inc.
3333 Highway 6 South, P.O. Box 4685, Houston, Texas 77251-7171, USA
Tel: +1 (281) 352-1475
Email: nicolas.tsesmetzis at shell.com<mailto:nicolas.tsesmetzis at shell.com>
Internet: http://www.shell.com/eandp-en

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20181114/aac3ec33/attachment-0001.html>