fobi_graph {fobitools} | R Documentation

## Generate FOBI Graphs

### Description

This function allows users to create networks based on FOBI relationships.

### Usage

    fobi_graph(
      terms = NULL,
      get = NULL,
      property = c("is_a", "BiomarkerOf", "Contains"),
      layout = "sugiyama",
      labels = FALSE,
      labelsize = 3,
      legend = FALSE,
      legendSize = 10,
      legendPos = "bottom",
      curved = FALSE,
      pointSize = 3,
      fobi = fobitools::fobi
    )

### Arguments

`terms` | A character vector with FOBI term IDs.
`get` | A character string indicating desired relationships between provided terms. Options are 'anc' (for ancestors) and 'des' (for descendants). Default is NULL and all information related with input terms will be provided.
`property` | A character vector indicating which properties should be plotted. Options are 'is_a', 'BiomarkerOf', and 'Contains'. By default all of them are included.
`layout` | A character string indicating the type of layout to create. Options are 'sugiyama' (default) and 'lgl'.
`labels` | Logical indicating if node names should be plotted or not.
`labelsize` | Numeric value indicating the size of labels.
`legend` | Logical indicating if legend should be plotted or not.
`legendSize` | Numeric value indicating the size of legend.
`legendPos` | A character string indicating the legend position (if legend parameter is set to TRUE). Options are 'bottom' (default) and 'top'.
`curved` | Logical indicating if the shape of the edges shape should be curved or not.
`pointSize` | Numeric value indicating the size of graph points.
`fobi` | FOBI table obtained with 'parse_fobi()'. If this value is set to NULL, the last version of FOBI will be downloaded from GitHub.

### Value

A ggraph object.

### Author(s)

Pol Castellano-Escuder

### References

Pol Castellano-Escuder, Raúl González-Domínguez, David S Wishart, Cristina Andrés-Lacueva, Alex Sánchez-Pla, FOBI: an ontology to represent food intake data and associate it with metabolomic data, Database, Volume 2020, 2020, baaa033, https://doi.org/10.1093/databa/baaa033.

### Examples

    terms <- c("CHEBI:16164","CHEBI:16243","FOODON:00001139","FOODON:00003274","FOODON:00003275")
    fobi_graph(terms, get = "anc")

    # Red meat related FOBI biomarkers
    fobi_graph(terms = "FOBI:0193",
               property = c("is_a", "BiomarkerOf"),
               layout = "lgl", curved = TRUE) # set labels = TRUE to display node names

[Package fobitools version 1.0.0 Index]