hpoPlot: Functions for Plotting HPO Terms

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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

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