hpoPlot: Functions for Plotting HPO Terms

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

View on CRAN

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...

Files in this package

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? 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.