Collection of functions for manipulating sets of HPO terms and plotting them with a various options.

Author | Daniel Greene <dg333@cam.ac.uk> |

Date of publication | 2015-12-14 12:07:27 |

Maintainer | Daniel Greene <dg333@cam.ac.uk> |

License | GPL (>= 2) |

Version | 2.4 |

**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...

hpoPlot

hpoPlot/inst

hpoPlot/inst/doc

hpoPlot/inst/doc/hpoPlot-guide.html

hpoPlot/inst/doc/hpoPlot-guide.Rmd

hpoPlot/inst/doc/hpoPlot-guide.R

hpoPlot/NAMESPACE

hpoPlot/data

hpoPlot/data/mpo.terms.RData

hpoPlot/data/mpo.to.hpo.RData

hpoPlot/data/hpo.terms.RData

hpoPlot/data/datalist

hpoPlot/R

hpoPlot/R/utils.R
hpoPlot/R/sets.R
hpoPlot/R/graphs.R
hpoPlot/R/data.R
hpoPlot/vignettes

hpoPlot/vignettes/hpoPlot-guide.Rmd

hpoPlot/MD5

hpoPlot/build

hpoPlot/build/vignette.rds

hpoPlot/DESCRIPTION

hpoPlot/man

hpoPlot/man/get.pop.frequency.based.colours.Rd
hpoPlot/man/intersection.with.branches.Rd
hpoPlot/man/get.descendants.Rd
hpoPlot/man/get.case.term.matrix.Rd
hpoPlot/man/simpleCap.Rd
hpoPlot/man/get.frequency.based.labels.Rd
hpoPlot/man/get.term.descendancy.matrix.Rd
hpoPlot/man/remove.terms.with.less.than.n.occurrences.Rd
hpoPlot/man/get.simple.node.labels.Rd
hpoPlot/man/hpo.terms.Rd
hpoPlot/man/swap.out.alt.ids.Rd
hpoPlot/man/get.informative.node.labels.Rd
hpoPlot/man/p.values.for.occurrence.of.term.in.group.Rd
hpoPlot/man/remove.links.Rd
hpoPlot/man/get.code.node.labels.Rd
hpoPlot/man/prune.branch.Rd
hpoPlot/man/get.mpo.to.hpo.Rd
hpoPlot/man/remove.uninformative.for.plot.Rd
hpoPlot/man/get.significance.based.sizes.Rd
hpoPlot/man/get.hpo.graph.Rd
hpoPlot/man/remove.uninformative.terms.Rd
hpoPlot/man/get.shortened.names.Rd
hpoPlot/man/setDimNames.Rd
hpoPlot/man/n.most.frequent.terms.Rd
hpoPlot/man/get.ancestors.Rd
hpoPlot/man/get.full.labels.Rd
hpoPlot/man/hpoPlot-package.Rd
hpoPlot/man/clean.terms.Rd
hpoPlot/man/get.term.pseudo.adjacency.matrix.Rd
hpoPlot/man/get.frequency.based.colours.Rd
hpoPlot/man/get.ontology.Rd
hpoPlot/man/mpo.terms.Rd
hpoPlot/man/get.case.based.colours.Rd
hpoPlot/man/get.node.friendly.long.names.Rd
hpoPlot/man/calibrate.sizes.Rd
hpoPlot/man/remove.non.pa.terms.Rd
hpoPlot/man/get.case.based.labels.Rd
hpoPlot/man/exclude.branch.Rd
hpoPlot/man/get.term.frequencies.Rd
hpoPlot/man/term.set.list.from.character.Rd
hpoPlot/man/apply.term.filters.Rd
hpoPlot/man/hpo.plot.Rd
hpoPlot/man/get.term.info.content.Rd
hpoPlot/man/get.frequency.based.sizes.Rd
hpoPlot/man/get.term.adjacency.matrix.Rd
hpoPlot/man/mpo.to.hpo.Rd
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.