load_data

Data loading

Here you find a detailed description how to load your data. The data can be provided in CSV/TXT format or as Excel (xls and xlsx) files. The different data tables include:

• ASV/OTU/MAG data: this is a matrix of ASV/OTU/MAG's in the rows and the abundance of the different sample in the columns. This is the core data and it can be of different form, e.g. integer value or relative abundance values. The different types of data can be processed further during the data loading process.
• Taxonomic data: similar to ASV data it is a matrix of ASVs in the rows but with different taxonomic levels as the colums. The number of rows must be similar to the ASV data.
• Sample data: This data contains describtion of samples represented as sample in the rows and different sample descriptions in the columns. The description can be study sites, sample depth or height or any other custom description or value that you want to use to groups your samples (e.g. for ordination).
• Sample management data/table: This table will be generated during the data loading and defines some details for plotting, e.g. color, symbol or label. However, if you want to reload you data you can use a custom file, that you generated earlier.
• Functional data ... coming soon
• Environmental data ... coming soon
• Combined upload (upload stored data) ... coming soon

Data formats

From experience we know that data loading is not trivial, as there are endless different formats. During data loading the R programming language often tries to guess the data format, e.g. numeric, character, data which often fails because of different storage and language specificities.

Our experience is that xlsx files cause fewest problems, except for some date and missing/NA values. Thus, we suggest to load xlsx files.

However, you can also load comma (CSV) or tab (tsv) seperated files or load text (TXT) with a common seperator.

ASV/OTU/MAG

The format of the ASV/OTU/MAG table must contain ASVs in the rows and samples in columns with stored abundance as values in the cells. The abundance values can be integers or floating point numbers, e.g. relative abundances.

First select Manage Data from the main menu and select Load data tables as shown in Figure 1.

The tab Count / Abundance data should be selected on the next page. Now you have to choose a local file to load by click Browse as shown in Figure 2.

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