Interomics is a application created to facilitate the visualization of metagenomic data. It is an user-friendly environment, where the user can easily: subset the data that is being calculated; select the variables that will be used to generate the plot, changing it instantly; visualize interactive plots – heatmap, alpha-diversity, beta-diversity – where you can obtain information by hovering the mouse over the plot, zoom in or out, isolate or hide groups in the plot based on specific characteristics; generate a taxonomic tree.
The program is available at the following link: https://aboffelli.shinyapps.io/interomics/.
The program is written in R (4.0.3), and uses the following packages:
- shiny 1.6.0
- metacoder 0.3.4
- phyloseq 1.34.0
- plotly 4.9.3
- BiocManager 1.30.12
- DT 0.18
The file sessionInfo.txt contains all the packages and versions used in the running session of the program.
Using Conda (4.9.2) you can create a new environment with all necessary packages with the following code on the terminal.
# Creates a conda env and downloads all the necessary packages
conda create -n interomics -c bioconda -c conda-forge r-base=4.0.3 r-dt bioconductor-phyloseq r-plotly r-metacoder r-shiny
# Activate the environment
conda activate interomics
# Start the R console in the terminal
RTo install the necessary package open the R console/Rstudio and use the lines below.
# Run each line separately.
packages <- c("shiny", "metacoder", "plotly", "BiocManager", "DT")
for(package in packages) install.packages(package)
BiocManager::install("phyloseq", ask=FALSE)The easiest way to run the program is directly from GitHub from the R console with the following command.
shiny::runGitHub("interomics", "aboffelli", ref="main")
# Optionally, you can select the port that will be used for the server (4 number digit).
shiny::runGitHub("interomics", "aboffelli", ref="main", port=xxxx)The error Error in utils::browseURL(appUrl) : 'browser' must be a non-empty character string may happen in your console. This means that R cannot open the browser automatically. To solve this error change the code above to the one below.
# Can also be used with the port selection
shiny::runGitHub("interomics", "aboffelli", ref="main", launch.browser=FALSE)This will prevent R from opening the browser automatically, just copy the URL that appears on the console and use it in your browser of preference.
If you opt for download the files from GitHub, the program consists in three files – ui.R, server.R, and global.R – that must be stored together in the same directory.
After the installation of the necessary packages and making sure that the three files – ui.R, server.R, and global.R – are together, you can run the program with the following line in the R console.
# The path below is an example, you may need to change it according to where the files are saved.
# It must point to the whole directory containing the three files mentioned before.
shiny::runApp("C:/User/Example/Interomics")
# The options of port selection and not opening the browser automatically can also be used.
shiny::runApp("C:/User/Example/Interomics", port=xxxx, launch.browser=FALSE)It is possible to load an example dataset selecting the checkbox Example dataset under the Load an example dataset area. When selected, the three example tables will be loaded and displayed.
The files can be uploaded in the initial page File Upload, where three files are required:
- OTU counts for each sample. The first column must contain the OTU name/number. The first row must contain the sample names.
- Taxonomic table for each OTU. The first column must contain the OTU name/number. The first row must contain the taxonomic levels.
- Sample data. The first column must contain the sample names. The first row will be read as a header.
The accepted formats are: plain-text (txt), comma-separated-values (csv), tab-delimited (tab/tsv). The type of separator can be defined in the File Upload page, the options are tab, comma, and semicolon. Make sure that all sample/OTU names are exactly the same in the three files, any difference in the names will end up in the removal of that sample/OTU.
The tables will be displayed in the right side, and updated according to the subset options, if activated. The tables are interactive, which means that you can: choose the number of entries to show, sort the rows based on the values of the column in ascending or descending order, search for an specific value.
The subset affects all the plots.
To subset the data, select the checkbox Use subset. The program will not use the filtered data if this checkbox is not selected, even if you chose the groups in the boxes. This checkbox can also be used to reset all the subset boxes, just by unchecking and checking again.
First, select if the target group will be isolated or removed from the data, using the radio buttons – Select/Remove – above the set of three boxes that you will use. Choose whether the group is in the Taxa or Sample tables to unlock the options in the level box, according to the table chosen. In the level box, choose the taxonomic level/column where the target group is located. Finally, select the target group in the last box.
Both options – select and remove – allow multiple target selection.
You can download the filtered tables, as tab delimited text files. The button Download subsetted data will download a tar file containing the three files.
To load the Heatmap, it is necessary to select a label for the samples.
The Heatmap is interactive, which means that you can zoom in by selecting an area inside the plot with the mouse, zoom out double clicking. Hovering the mouse over the plot gives you the information about the sample name, the OTU number, and the abundance. In the top right corner of the plot you will find some command buttons, including: save the plot as a png image, selection box, zoom in and out, reset axes, etc. Click the button Download to download the original plot as pdf – any interactive change, such as zoom or hidden objects, will not be present.
In the Taxonomic Tree tab, you will find a slide bar where you can select the minimum abundance to be considered in the tree, as well as a filtering option similar to the subset area. To use the filter option, first select the taxonomy level that the target group is located, all the possible groups in that level will be available to selection in the next box. As the data can be heavy, the image will only be created after clicking the button Create tree. The image may take a while to be displayed.
To download the taxonomic tree in pdf format, click the button Download.
Only the X variable and the Measures are required for the Alpha-Diversity plot. The Color and Shape variables are optional, if not selected, all samples will be colored black and shaped as circles. You can select multiple types of measure, each of them will be displayed side by side.
The slider can be used to trim the data for the alpha-diversity calculation. OTUs with the abundance equal to or lower than the number selected will be removed for the calculation.
The Alpha-Diversity plot is interactive, which means that you can zoom in selecting an area inside the plot with the mouse, zoom out double clicking. Hovering the mouse over the plot gives you the information about the selected variables and value of the measure selected. You can hide a group by clicking on the legend corresponding to that group in the right side, or isolate a group by double clicking in the legend corresponding to the group. In the top right corner of the plot you will find some command buttons, including: save the plot as a png image, selection box, zoom in and out, reset axes, etc. Click the button Download to download the original plot as pdf – any interactive change, such as zoom or hidden objects, will not be present.
All variables, type, color and shape, are required to create the Beta-Diversity plot. The type selection defines which variables can be chosen in the color and shape boxes. The type taxa will only allow variables from the Taxonomic table; the sample type will only allow Sample table variables; the biplot and split will allow all variables from both Taxonomic and Sample tables. The biplot and split are the same plot, however in the split option the samples and taxa are split to facilitate the analysis.
The Beta-diversity plot is interactive, which means that you can zoom in selecting an area inside the plot with the mouse, zoom out double clicking. Hovering the mouse over the plot gives you the information about the selected variables and the positions NMDS1 and NMDS2. You can hide a group by clicking on the legend corresponding to that group in the right side, or isolate a group by double clicking in the legend corresponding to the group. In the top right corner of the plot you will find some command buttons, including: save the plot as a png image, selection box, zoom in and out, reset axes, etc. Click the button Download to download the original plot as pdf – any interactive change, such as zoom or hidden objects, will not be present.