hpoPlot: Functions for Plotting HPO Terms
Version 2.4

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

AuthorDaniel Greene <dg333@cam.ac.uk>
Date of publication2015-12-14 12:07:27
MaintainerDaniel Greene <dg333@cam.ac.uk>
LicenseGPL (>= 2)
Version2.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("hpoPlot")

Getting started

Package overview
Plotting HPO Phenotypes

Popular man pages

get.case.based.colours: Function to set colours of HPO nodes in plot to distinguish...
get.hpo.graph: Get HPO graph object
get.node.friendly.long.names: Split up the HPO term descriptions so they fit in nodes for...
get.term.pseudo.adjacency.matrix: Get an adjacency to MRCA matrix for set of HPO terms
hpo.plot: Plot HPO graph object
mpo.terms: MPO Terms object
mpo.to.hpo: Object containing data for mapping between MPO and HPO
See all...

All man pages Function index File listing

Man 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...
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...

Functions

ancs.from.pars Source code
apply.term.filters Man page Source code
calibrate.sizes Man page Source code
clean.terms Man page Source code
exclude.branch Man page Source code
get.ancestors Man page Source code
get.case.based.colours Man page Source code
get.case.based.labels Man page Source code
get.case.term.matrix Man page Source code
get.code.node.labels Man page Source code
get.descendants Man page Source code
get.frequency.based.colours Man page Source code
get.frequency.based.labels Man page Source code
get.frequency.based.sizes Man page Source code
get.full.labels Man page Source code
get.hpo.graph Man page Source code
get.informative.node.labels Man page Source code
get.mpo.to.hpo Man page Source code
get.node.friendly.long.names Man page Source code
get.ontology Man page Source code
get.pop.frequency.based.colours Man page Source code
get.shortened.names Man page Source code
get.significance.based.sizes Man page Source code
get.simple.node.labels Man page Source code
get.term.adjacency.matrix Man page Source code
get.term.descendancy.matrix Man page Source code
get.term.frequencies Man page Source code
get.term.info.content Man page Source code
get.term.pseudo.adjacency.matrix Man page Source code
hpo.plot Man page Source code
hpo.terms Man page
intersection.with.branches Man page Source code
mpo.terms Man page
mpo.to.hpo Man page
n.most.frequent.terms Man page Source code
p.values.for.occurrence.of.term.in.group Man page Source code
prune.branch Man page Source code
remove.links Man page Source code
remove.non.pa.terms Man page Source code
remove.terms.with.less.than.n.occurrences Man page Source code
remove.uninformative.for.plot Man page Source code
remove.uninformative.terms Man page Source code
setDimNames Man page Source code
simpleCap Man page Source code
str.ancs.from.pars Source code
swap.out.alt.ids Man page Source code
term.set.list.from.character Man page Source code

Files

inst
inst/doc
inst/doc/hpoPlot-guide.html
inst/doc/hpoPlot-guide.Rmd
inst/doc/hpoPlot-guide.R
NAMESPACE
data
data/mpo.terms.RData
data/mpo.to.hpo.RData
data/hpo.terms.RData
data/datalist
R
R/utils.R
R/sets.R
R/graphs.R
R/data.R
vignettes
vignettes/hpoPlot-guide.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/get.pop.frequency.based.colours.Rd
man/intersection.with.branches.Rd
man/get.descendants.Rd
man/get.case.term.matrix.Rd
man/simpleCap.Rd
man/get.frequency.based.labels.Rd
man/get.term.descendancy.matrix.Rd
man/remove.terms.with.less.than.n.occurrences.Rd
man/get.simple.node.labels.Rd
man/hpo.terms.Rd
man/swap.out.alt.ids.Rd
man/get.informative.node.labels.Rd
man/p.values.for.occurrence.of.term.in.group.Rd
man/remove.links.Rd
man/get.code.node.labels.Rd
man/prune.branch.Rd
man/get.mpo.to.hpo.Rd
man/remove.uninformative.for.plot.Rd
man/get.significance.based.sizes.Rd
man/get.hpo.graph.Rd
man/remove.uninformative.terms.Rd
man/get.shortened.names.Rd
man/setDimNames.Rd
man/n.most.frequent.terms.Rd
man/get.ancestors.Rd
man/get.full.labels.Rd
man/hpoPlot-package.Rd
man/clean.terms.Rd
man/get.term.pseudo.adjacency.matrix.Rd
man/get.frequency.based.colours.Rd
man/get.ontology.Rd
man/mpo.terms.Rd
man/get.case.based.colours.Rd
man/get.node.friendly.long.names.Rd
man/calibrate.sizes.Rd
man/remove.non.pa.terms.Rd
man/get.case.based.labels.Rd
man/exclude.branch.Rd
man/get.term.frequencies.Rd
man/term.set.list.from.character.Rd
man/apply.term.filters.Rd
man/hpo.plot.Rd
man/get.term.info.content.Rd
man/get.frequency.based.sizes.Rd
man/get.term.adjacency.matrix.Rd
man/mpo.to.hpo.Rd
hpoPlot documentation built on May 19, 2017, 4:40 p.m.

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