CCA/RDA analysis





Select a file  example file

Select a file   example file

Select a file   example file



















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 The number of coins consumed at one time is 2



Function:
A multivariate constrained ordination technique that extracts major gradients among combinations of explanatory variables in a dataset.


Input:
1. enter file:
(1)The input file can be OTU table with taxonomic annotation (required)
(2)The environment gradient (factor) table, number of factors should be less or equal to sample number (required)
(3)Grouping file is optional. The tool supports no more than 2 grouping information in a single sample.
(4) The input file should be a tab-delimited “.txt” file.


Parameters:


Analysis type:

define an analysis method, matrix can be analysis using CCA or RDA model


Taxon name:

to show taxon (ie. Genus) name on the plot


Top taxon:

to show how many top abundant taxon on the plot


Graph title:

define a graph title


Dot size:

define the dots size.


Dot transparency:

define the dots transparency if case of overlapping of dots.


Group color representation (color number should be equal to group number)

define the color representation of each group, color number should be equal to group number


输出:
1)CCA_sample_sites.xls:document the sum of all eigenvalues and importance of each axis
2)CCA_species_sites:document taxon dot sites in a CCA/RDA plot.
3)CCA_envir-factor_sites:document environmental factor(gradient) dot sites in a CCA/RDA plot
4)DCA.summary:summarize a DCA analysis result

5)environmental factor correlation table:summarize the correlation between environmental factor and RDA axis

6)CCA/RDA graph:

CCA1-2.nonlabs.png/pdf: A CCA/RDA plot without sample names
CCA1-2.png/pdf: A CCA/RDA plot with sample names

example :
Input:OTU table  Environmental factor table  group file


Output:
1:CCA_sample_sites.xls
Samples CCA1  CCA2  CCA3  CCA4  CCA5  CA1
CK1 -1.17237086899951 0.231164561576716 2.43536547360125  0.468613538470372 -0.521936162667495  -0.808046986758666
CK2 -1.1572665823102  -1.42860877240687 -0.549032209802859  2.83351063677702  1.43378119851602  2.02534821080922
CK3 -1.49570686760746 0.0273462956558565  -0.706329227389229  0.865838710760632 -0.290912650451685  1.01877976615298
CK4 -1.20710868460347 0.370935253362443 -2.60560316720684 -2.42810618842451 0.168506841308157 -1.6719608268434
CK5 -1.5562702802342  0.651269590349488 0.595882020371293 -1.45146930145046 -0.318000696274572  -0.251630348306944
CA1 0.974610196394923 -0.104745619111151  -0.334203278424584  1.04120295623205  -0.0531562686390503 -0.942931875531439
CA2 0.760730059809399 -2.12637958035229 0.745781118766851 -1.63166065483332 -0.0165817224481634 -0.573209913163789
CA3 0.80435142753797  0.700368060885899 -0.263211126786403  0.229812203163464 -1.61999680223531 0.0204114357736938
CA4 0.567093187244471 0.262752025306537 0.0148235934121042  -0.437995730700719  -0.822034862380148  0.231909808702752
CA5 0.700914846513469 1.98976523732017  -0.162807163417265  0.0466015118241849  3.06827940812714  1.3262899501884
        

2:CCA_species_sites
Species CCA1  CCA2  CCA3  CCA4  CCA5  CA1
Alicyclobacillus  0.34595108156025  -0.249931443439814  -0.00508892535787803  0.0575514559218589  -0.0294336770660223 -0.168446818978494
Bacillus  -0.434908707180272  0.110247143354924 0.143966641687111 -0.0483216220508095 -0.0280734921997281 -0.0313666148504983
CandidatusRhabdochlamydia 0.332412329234085 0.149552158756664 -0.110963677277933  -0.00513846687288351  -0.0755745296229585 0.0185259066401049
CandidatusSolibacter  -0.338931730698679  0.0879930888338368  -0.0635812894580597 -0.220352060529118  -0.00527399612415062  -0.0720185430737823
Mycobacterium 0.30769780457627  0.109805580124376 0.0324946604566324  0.015709933373511 0.251544295518129 0.0327943021149191
Acidobacterium  0.593748839228754 0.413222114904331 -0.0190275868032072 0.0499162197773069  0.154477266462497 0.146438254658603
CandidatusKoribacter  -0.807533540490883  -0.238088566626537  -0.166963852695348  0.255945631985289 0.07726025494122  0.691926396129785
Conexibacter  0.682330827072613 0.380118852507714 0.0317777784942295  -0.0492734196140707 0.000966010984764718  0.205043073765086
Nocardioides  -0.820114462482764  0.0737283559695164  0.673717900416305 0.279984911111747 0.0122300186916335  0.036916331507856
Pilimelia -1.27268641146115 -0.0237692247359973 -0.375484360703181  -0.0268117477942791 0.0397218484000157  -0.0137762143280586
Sinomonas -1.1647948301215  -0.0991385843491781 -0.140260843226405  0.265065165234655 -0.058581660637485  0.625884640720445
Streptomyces  -0.706743539907205  -0.0165173955314497 -0.210856929356171  -0.0941302900650263 0.027518630271319 0.102114406891466
Flavobacterium  0.197779672222041 -1.21998311475552 0.276998901549968 -0.4668873108256  0.147784962249983 0.0874168205447417
Kitasatospora -0.513045251422147  -0.426617698321745  -0.149095388924391  0.188923417085328 0.176398426958694 0.490444761685818
Parachlamydia 0.490302339839949 0.0763178809781672  -0.126739126101196  -0.0644678365797921 -0.240110777182143  0.0305911858454124
Rathayibacter 0.543807338526059 0.155078631329423 0.19654117415888  0.0411930207557103  0.151295881530674 -0.0191993792585311
Edaphobacter  0.499205261603634 0.353178206304564 0.0594334945395013  -0.116917048551099  0.283954689966612 0.41768442620536
Catellatospora  -1.41823522496713 -0.127184907485305  -1.38322918921647 -0.398764248425288  0.174072239090334 -0.655892489276133
Virgisporangium -1.3141321649437  -0.0283163960812968 -1.07500687863742 -0.394924480802182  0.13068384248966  -0.783230745347689
Prevotella  0.719998724070353 -1.50861319724635 0.529239772332071 -1.03135529651776 0.213618328885839 -0.564226755041147
        

3:CCA_envir-factor_sites
Constrain CCA1  CCA2  CCA3  CCA4  CCA5  CA1
AN  0.215918459134623 0.300454636633771 0.0037843269271663  0.189483055402639 -0.909498807539178  0
AP  -0.88321103447841 -0.00780260484008147  0.179211133562975 0.393625808498019 0.18116147610527  0
AK  -0.948073637913666  0.0805585577858008  0.294316730344931 0.066086075520977 0.0606381787484189  0
OM  -0.256087308224969  0.643580255179155 0.0716367791250762  0.502223686811577 0.51270194654555  0
Ph  -0.945408617807588  -0.0121426079324861 -0.30469138398077 -0.0743625293392954 0.0876839620791046  0
        

4:DCA.summary
DCA Eigenvalues Decorana_values Axis_lengths
DCA1  0.235586191937275 0.24189609354078  2.04870842887944
DCA2  0.080053434386399 0.046972558162257 2.25698204351043
DCA3  0.0563583935717481  0.0158306521768173  1.47759325956464
DCA4  0.0261967709460555  0.00724315524884521 1.65694736271154
        

5:environmental factor correlation table
Constrain RDA1_cos  RDA2_cos
AN  0.583576682528919 0.812058037093742
AP  -0.999960979319677  -0.00883401596283277
AK  -0.996409414613128  0.0846656864988553
OM  -0.369716370113742  0.929144663478147
Ph  -0.999917529028949  -0.0128427076833458
        



CCA/RDA graph::
生物云平台
生物云平台