Plotting Ontological Terms

library(ontologyIndex)
library(ontologyPlot)
data(hpo)

Plotting Terms

A set of terms (character vector of term IDs) can be plotted as a subgraph of the ontology by calling onto_plot:

onto_plot(hpo, terms=c("HP:0001873", "HP:0011877"))

To include all ancestral terms, use the get_ancestors function:

onto_plot(hpo, terms=get_ancestors(hpo, c("HP:0001873", "HP:0011877")))

The function remove_links can be used to remove terms simply linking two terms together, thus the structure of the given part of the ontology can be retained whilst simplifying the figure:

onto_plot(hpo, terms=remove_links(hpo, get_ancestors(hpo, c("HP:0001873", "HP:0011877"))))

Graphical parameters

Graphical attributes to assign to each node can be passed to onto_plot. The graphical attributes can be specified as:

• a single value, thus setting the attribute to the given value for all nodes,
• a vector the same length as the terms argument, so the ith term gets the ith attribute value,
• a function which returns the desired attribute value for each term.

Node attributes which affect the plot generated include those supported by the Rgraphviz package. Some of these include:

• fillcolor - the colour to use for each node,
• color - the colour for the border of the node (defaults to "transparent"),
• label - a character vector of term IDs to be used as the labels,
• fontsize - font size of label text printed in each term,
• width - the relative width of the nodes.

In this example, we pass the term IDs as the labels and a character vector of colours generated with rainbow to colour the nodes.

terms <- remove_links(hpo, get_ancestors(hpo, c("HP:0001873", "HP:0011877")))
onto_plot(hpo, terms=terms, label=terms, fillcolor=rainbow(length(terms)))

ontologyPlot contains several functions for setting the graphical parameters which can be passed to onto_plot. These include for example label_by_frequency, official_labels and label_by_term_set (see individual help files for more details).

These functions must accept an ontology and terms argument. They can optionally accept:

• frequencies: a numeric vector of population frequencies named by term,
• term_sets: a list of character vectors of terms [i.e. annotated objects] arguments.

If any of the given functions require these additional arguments, they must be passed to onto_plot.

Frequencies

A frequencies argument giving a population frequency of terms can be passed to onto_plot. If this argument is passed, functions which make use of it in determining graphical parameters can be passed to onto_plot, for instance colour_by_population_frequency.

frequencies <- seq(from=0, to=1, by=1/length(terms))
names(frequencies) <- terms
onto_plot(hpo, terms=terms, frequencies=frequencies, 
    fillcolor=colour_by_population_frequency)

Term sets

Another argument which can be passed to onto_plot is term_sets, a list of sets of ontological terms (e.g. a set of HPO encoded phenotypes). If terms_sets is given, the terms parameter of onto_plot defaults to the value of remove_uninformative_terms(ontology, term_sets), which removes terms which are annotated to exactly the same objects as all of their children (with the effect of greatly simplifying the resulting diagram - see ?remove_uninformative_terms for more details).

hpo_phenotypes <- list(
    A=c("HP:0001382","HP:0004272","HP:0007917","HP:0004912","HP:0001596"),
    B=c("HP:0001382","HP:0004272","HP:0002165","HP:0004800","HP:0004912"),
    C=c("HP:0004800","HP:0001382","HP:0004912","HP:0007917","HP:0008743")
)

onto_plot(hpo, term_sets=hpo_phenotypes, label=label_by_term_set)

To further decorate the plot, we could use the frequency of each term in hpo_phenotypes them to colour them.

onto_plot(
    hpo,    
    frequencies=get_term_frequencies(hpo, hpo_phenotypes),
    term_sets=hpo_phenotypes,
    label=label_by_term_set,
    fillcolor=colour_by_frequency)

Edge attributes

Edge attributes recognised by Rgraphviz can also be supplied by the edge_attributes argument.

onto_plot(
    hpo,    
    frequencies=get_term_frequencies(hpo, hpo_phenotypes),
    term_sets=hpo_phenotypes,
    label=label_by_term_set,
    edge_attributes=list(color="red", lty="dashed"))

Plots for publications

To get the highest quality plots and fine-grained control over the node and edge attributes, the best option is to create the ontological_plot with onto_plot and write it to a file in dot format using the write_dot function. The file can then be opened using a layout program, for example the graphviz program (http://www.graphviz.org/), to visualise/export as an image. Individual node and edge attributes can then be modified by editing the file.