R Shiny Application

An R shiny application is created from results of the MetaFunc run. The homepage of the application is shown as follows:

_images/RShiny.png

Fig. 2 R Shiny Homepage


Usage

Note

RStudio is needed to launch the visualisation application.

The MetaFunc repository comes with a metafunc-shiny directory that contains all the dependecies of the application. The MetaFunc pipeline will produce a metafunc-shiny/metafunc_results/ with a database file *.db within at the end of the run, based on results of analyses performed by MetaFunc. The application may then be launched as follows:

  1. If the run was done remotely, the user may first have to download the metafunc-shiny directory onto their local computer

  2. Launch the metafunc-shiny.Rproj in the metafunc-shiny directory in Rstudio.

  3. Open the app.R file in RStudio.

  4. Run the app in RStudio.

  5. Explore results (see Display)

Viewing Results of Different Runs

To view different runs in the app, the user would have to ensure the following:

  1. The database (*.db) file is in the /data/ folder of the metafunc-app directory. Databases will be placed here automatically.

  2. In the home page of the app, select the database that corresponds to the run and press “Load Database”.


Display

The following tables are opened in the R Shiny Application and may be explored by the user:

Microbiome

R Shiny displays the following tables straight from the MetaFunc pipeline (Figure 3):

_images/RShiny_Microbiome.png

Fig. 3 R Shiny Microbiome Tables Generated

  1. Taxonomy (DIR: analyses/results/microbiome/taxonomy)

    1.1 per_sample/all_sptableScaled.tsv

    1.2 per_group/grouped_sptable_pct.tsv

At the top of the page, the user can toggle between Individual or Grouped samples (Figure 4, red box), and choose which columns to include in the view (Figure 4, green box). The user can also search for specific species (4, yellow box) and download the resulting table as .csv or excel file (4, blue box)

_images/RShiny_MicTax.png

Fig. 4 R Shiny Microbiome Taxonomy Table Options

  1. Function (DIR: analyses/results/microbiome/function)

    2.1 per_sample/all_samples_goPercent.tsv

    2.2 per_group/all_grouped_goPercent.tsv

Similar to Taxonomic abundances, the user can also toggle between Individual or Grouped samples, choose which columns to include in the view, search for specific GO terms, and download resulting tables (same color boxes as Figure 4). In addition, the user would be able to choose among the following GO namespaces (Figure 5, purple box): Biological Process (BP), Molecular Function (MF), and Celluar Component (CC).

_images/RShiny_GO.png

Fig. 5 R Shiny Microbiome GO Options


R Shiny also generates the following tables that link GOs to TaxIDs and vice versa (Figure 3):

  1. GO to TaxIDs

The user can select one or more GO terms (Figure 6, upper box) and the MetaFunc R Shiny Application will provide the species who have proteins annotated with the GO(s) in question, with their corresponding abundances (Figure 6, lower box). Along with the viewing options described above, this page includes another toggle, Toggle Inclusivity Selection of TaxIDs (Figure 6, grey box) so users can choose to include either all the species that are annotated with any of GOs selected (In Any) or only the species annotated with all the GOs selected (Only in All). The resulting species table may also be downloaded as .csv or excel file.

_images/RShiny_GO2Tax.png

Fig. 6 R Shiny Microbiome GO to TaxID Example. GO selected is polyamine biosynthetic process and shown in the Figure are species with proteins annotated with the GO term.

  1. TaxIDs to GOs

Conversely, the user can select one or more species (Figure 7, upper box) and the Metafunc R Shiny application will provide the GO terms annotating the proteins of the selected species, with their corresponding abundances (Figure 7, lower box). The same viewing options as GO to TaxIDs are included. The resulting GO table may also be downloaded as .csv or excel file.

_images/RShiny_Tax2GO.png

Fig. 7 R Shiny Microbiome TaxID to GO Example. Species selected is Bacteroides fragilis and shown in the Figure are GOs annotating the proteins of B. fragilis.


Host

R Shiny also displays host gene abundances as transcripts-per-million (Figures 8 and 9)

_images/RShinyHost.png

Fig. 8 R Shiny Host Table Generated


For the host table, the user can select which columns to include in the view (Figure 9, green box), search for specific genes (Figure 9, yellow box), and download the resulting table as .csv or excel file (Figure 9, blue box).

_images/RShiny_HostSample.png

Fig. 9 R Shiny Host Table Options