Functions for Plotting HPO Terms
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘hpoPlot’ version 2.4
Help Pages
| 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 character vector of terms |
| 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 terms belonging to different sets of phenotypes |
| get.case.based.labels | Function to label HPO nodes in plot to indicate to which phenotypes each of the terms belong |
| 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 frequency with which terms appear in phenotypes |
| get.frequency.based.labels | Function to label HPO nodes in plot based on frequency of occurrence in phenotypes |
| get.frequency.based.sizes | Function to size HPO nodes in plot based on frequency of occurrence in phenotypes |
| 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 information content |
| 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 plot |
| 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 information content/frequency of terms with respect to population |
| 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 significance of seeing this many of each term in phenotypes |
| get.simple.node.labels | Function to label HPO nodes in plot with just node description |
| 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 |
| 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 phenotypes |
| p.values.for.occurrence.of.term.in.group | Get p-values for observing at least as many of each term as have been in phenotypes given information content |
| prune.branch | Prune all terms descending from given term down to that term and ensure no degeneracy |
| 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 set of phenotypes |
| setDimNames | setNames for arrays... |
| simpleCap | Capitalise words in character vector |
| swap.out.alt.ids | Remove alternate/deprecated HPO term IDs and swap for new ones |
| term.set.list.from.character | Get list of character vector of HPO terms, given character vector of comma separated terms |