The format of sample files for uploading is as follows.
You can download abundance data and meta data .
Abundance data
Meta data
The second column is group information, named 'Group'.Beta diversity mapping description
Upload sample data
You need to upload two data files including sample OTU result file and metadata file.
Such as
| Sample | Achimill | Agrostol | Airaprae | Alopgeni | Anthodor | Bellpere | Bromhord | Chenalbu | Cirsarve | Comapalu | Eleopalu | Elymrepe | Empenigr | Hyporadi | Juncarti | Juncbufo | Lolipere | Planlanc | Poaprat | Poatriv | Ranuflam | Rumeacet | Sagiproc | Salirepe | Scorautu | Trifprat | Trifrepe | Vicilath | Bracruta | Callcusp |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 7 | 0 | 4 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 2 | 3 | 0 | 0 | 2 | 0 | 3 | 4 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 5 | 0 | 4 | 7 | 0 | 0 | 0 | 0 | 5 | 0 | 5 | 0 | 0 | 0 |
| 3 | 0 | 4 | 0 | 7 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 6 | 0 | 5 | 6 | 0 | 0 | 0 | 0 | 2 | 0 | 2 | 0 | 2 | 0 |
| 4 | 0 | 8 | 0 | 2 | 0 | 2 | 3 | 0 | 2 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 5 | 0 | 4 | 5 | 0 | 0 | 5 | 0 | 2 | 0 | 1 | 0 | 2 | 0 |
| 5 | 2 | 0 | 0 | 0 | 4 | 2 | 2 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 2 | 5 | 2 | 6 | 0 | 5 | 0 | 0 | 3 | 2 | 2 | 0 | 2 | 0 |
The first column is the sample id,the other column is the abundance of each indicator in different samples.
| Sample | group |
|---|---|
| 1 | SF |
| 2 | BF |
| 3 | SF |
| 4 | SF |
| 5 | HF |
| 6 | HF |
| 7 | HF |
| 8 | HF |
| 9 | HF |
The first column is the sample id,the second column is the grouping of samples.
Paying attention, please ,you need to upload the file in the format of the sample data.
Different beta diversity analysis tools
Different drawing tools
PCoA
Dissimilarity index, partial match to “manhattan”, “euclidean”, “canberra”, “clark”, “bray”, “kulczynski”, “jaccard”, “gower”, “altGower”, “morisita”, “horn”, “mountford”, “raup”, “binomial”, “chao”, “cao”, “mahalanobis”, “chisq” or “chord”.
The Jaccard and Bray-curtis dissimilarity coefficients are commonly used in bioinformatics analysis and are the basis for calculating species similarity.
It should be noted that the focus of these two dissimilarity coefficients is different.
In analysis, Jaccard only considers the presence or absence of species in the sample, not the abundance.
The Bray-curtis calculation not only considers the presence or absence of species in the sample, but also considers the relative abundance of different species.
This button can choose whether to perform R-value and P-value calculations on the data. R2 can quantify the strength of the relationship between the model response variable and the dependent variable. The p-value test can determine how reliable the fitted equation is.
PCA
Whether to add labels to each point
Adjust label position
Adjust label font size
Adjust the aspect ratio of the drawing
NMDS
The function offers different standardization methods for community data:
Dissimilarity index, partial match to “manhattan”, “euclidean”, “canberra”, “clark”, “bray”, “kulczynski”, “jaccard”, “gower”, “altGower”, “morisita”, “horn”, “mountford”, “raup”, “binomial”, “chao”, “cao”, “mahalanobis”, “chisq” or “chord”.It is the same as PCA distance matrix method.
About MicrobioSee
MicrobioSee, a web-based community microbial metagenome visualization toolkit developed in this study can be used on all operating system platforms that support modern browsers, and MicrobioSee provides data mining and visualization services for the field of microbial integration research.
The detail of MicrobioSee at here.
Less is more.
Contact us
PI:Chengjian Jiang
Guangxi Research Center for Microbial and Enzyme Engineering Technology College of Life Science and Technology, Guangxi University, Nanning 530004, China.
E-mail: jiangcj@gxu.edu.cn
Update Log
2021-12-15 We developed a Windows client for MicrobioSee,and macos version is being developed.
2021-11-23 We have completed the migration of all services. After that, the update log is moved to the Instruction
2021-11-17 The tutorials were made into videos posted on YouTube and Bilibili.
2021-11-14 Debuged the Stacked Bar Charts.
2021-11-10 Sorted out the code and added the funciton of upset map
2021-11-03 Completed documentation of instructions. Fixed known bugs.
2021-9-1 Major development work completed.
