Functions for Plotting HPO Terms

apply.term.filters | Apply a list of term filters to a given plotting context |

calibrate.sizes | Function to scale sizes of terms between two given limits |

clean.terms | Remove redundant/implied terms |

exclude.branch | Exclude terms descending from particular term from a... |

get.ancestors | Get set of all ancestors of set of terms |

get.case.based.colours | Function to set colours of HPO nodes in plot to distinguish... |

get.case.based.labels | Function to label HPO nodes in plot to indicate to which... |

get.case.term.matrix | Get a matrix with columns of hpo terms and rows of patients, |

get.code.node.labels | Function to label HPO nodes in plot with just HPO code |

get.descendants | Get set of all descendants of single term |

get.frequency.based.colours | Function to colour HPO nodes in plot with colours based on... |

get.frequency.based.labels | Function to label HPO nodes in plot based on frequency of... |

get.frequency.based.sizes | Function to size HPO nodes in plot based on frequency of... |

get.full.labels | Function to label HPO nodes in plot with full labels |

get.hpo.graph | Get HPO graph object |

get.informative.node.labels | Function to label HPO nodes in plot with node description and... |

get.mpo.to.hpo | Get MPO to HPO R-Object |

get.node.friendly.long.names | Split up the HPO term descriptions so they fit in nodes for... |

get.ontology | Get R-Object representation of ontology from obo file |

get.pop.frequency.based.colours | Function to colour HPO nodes in plot with colours based on... |

get.shortened.names | Get human readable, shortened (where possible) HPO term names |

get.significance.based.sizes | Function to size HPO nodes in plot with colours based on... |

get.simple.node.labels | Function to label HPO nodes in plot with just node... |

get.term.adjacency.matrix | Get an adjacency for set of HPO terms |

get.term.descendancy.matrix | Get logical descendancy matrix for set of terms |

get.term.frequencies | Get frequency of each term in a set of phenotypes |

get.term.info.content | Get information content of each term in a set of phenotypes |

get.term.pseudo.adjacency.matrix | Get an adjacency to MRCA matrix for set of HPO terms |

hpo.plot | Plot HPO graph object |

hpoPlot-package | Functions for Plotting HPO Terms |

hpo.terms | HPO Terms object (based on version 887 of the HPO) |

intersection.with.branches | Intersect set of terms with branches of HPO |

mpo.terms | MPO Terms object |

mpo.to.hpo | Object containing data for mapping between MPO and HPO |

n.most.frequent.terms | Select most frequently annotated terms from a set of... |

prune.branch | Prune all terms descending from given term down to that term... |

p.values.for.occurrence.of.term.in.group | Get p-values for observing at least as many of each term as... |

remove.links | Remove terms with exactly one parent and child from plot |

remove.non.pa.terms | Remove terms not descending from phenotypic abnormality |

remove.terms.with.less.than.n.occurrences | Remove terms with less than certain number of occurrences |

remove.uninformative.for.plot | Remove uninformative terms (fitting plotting filter format) |

remove.uninformative.terms | Get a minimal set of terms which can be used to partition a... |

setDimNames | setNames for arrays... |

simpleCap | Capitalise words in character vector |

swap.out.alt.ids | Remove alternate/deprecated HPO term IDs and swap for new... |

term.set.list.from.character | Get list of character vector of HPO terms, given character... |

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