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...

Functions

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

Files

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.