What Files Do I Need?

1. An SVG image of the site broken down into paths or regions.
2. Tab-delimited text file, such as the tab-delimited files produced by QIIME [1] (e.g., summarized taxa, alpha- and beta-diversity files, etc.).

SVG Image (.svg)

The following shows an SVG image of the hand, where the image is comprised of paths.

Tab-delimited text file (.txt)

The metadata files are tab-delimited files, which are illustrated by the following examples of a summarized taxonomy and principal coordinates files produced from QIIME.

Example 1: Summarized Taxonomy File

The following is a summarized taxonomy file produced from QIIME. The first column contains the SampleID’s which allow for correspondence to the paths of the SVG image, while the remaining columns consist of relative abundance of specific taxa in each region of the hand.

SampleID Root;k__Bacteria;p__Acidobacteria Root;k__Bacteria;p__Actinobacteria Root;k__Bacteria;p__Bacteroidetes Root;k__Bacteria;p__Chloroflexi
Hand23   0.000245761                       0.762349472                        0.010076186                       0.00098304
Hand24   0                                 0.707366297                        0.012865792                       0.000756811
Hand25   0.000254453                       0.844020356                        0.005343511                       0.001017812
Hand26   0                                 0.842782152                        0.003674541                       0
Hand27   0.000412201                       0.819455894                        0.002061006                       0.000412201
Hand28   0.000236574                       0.814289094                        0.007097232                       0.000709723
Hand29   0.000546001                       0.870870871                        0.011739012                       0
Hand30   0.027284827                       0.725598935                        0.008651287                       0.007542147
Hand31   0                                 0.788298347                        0.006252791                       0
Hand32   0.001885607                       0.79698303                         0.009679447                       0.001005657

Example 2: Principal Coordinates File

The following is a weighted Unifrac principal coordinates file produced from QIIME. The first column contains the SampleID’s which allow for correspondence to the paths of the SVG image, while the remaining columns consist of the values for each principal coordinate vector (PC 1-5) at each region of the hand.

pc vector number 1            2            3            4            5
Hand23            0.017674734  0.086331264  0.04473723   0.004003589  0.011900936
Hand24            0.03721532   0.114295555  0.026545593  0.031769352 -0.003194077
Hand25            0.02641303  -0.048601292  0.010150082 -0.027385228 -0.000666115
Hand26            0.052684939 -0.02055477  -0.016175269 -0.005657196  0.004005854
Hand27            0.084910157 -0.059976555 -0.009576943  0.019973765 -0.00334975
Hand28           -0.050264269 -0.020207926  0.050633036 -0.019990939  0.005436556
Hand29           -0.007034615  0.007534214 -0.01853336  -0.016552325 -0.038254278
Hand30            0.16615244   0.069815221  0.007417206  0.106767431 -0.044294094
Hand31            0.083281617  0.058672536 -0.01844925  -0.017083253  0.036211152
Hand32            0.071622503  0.027033638  0.043880704  0.028824731  0.010783767

References

[1]

Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Pena, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J. and Knight, R. (2010) QIIME allows analysis of high-throughput community sequencing data, Nat Methods, 7, 335-336.