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hpoPlot (version 2.2)
Functions for Plotting HPO Terms
Description
Collection of functions for manipulating sets of HPO terms and plotting them with a various options.
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Install
install.packages('hpoPlot')
Monthly Downloads
58
Version
2.2
License
GPL (>= 2)
Maintainer
Daniel Greene
Last Published
August 26th, 2015
Functions in hpoPlot (2.2)
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get.node.friendly.long.names
Split up the HPO term descriptions so they fit in nodes for plot
mpo.terms
MPO Terms object
get.white.nodes
Function to colour HPO nodes in plot white
term.set.list.from.character
Get list of character vector of HPO terms, given character vector of comma separated terms
remove.terms.with.less.than.n.occurrences
Remove terms with less than certain number of occurrences
get.term.descendancy.matrix
Get logical descendancy matrix for set of terms
hpoPlot
Functions for Plotting HPO Terms
get.term.adjacency.matrix
Get an adjacency for set of HPO terms
remove.non.pa.terms
Remove terms not descending from phenotypic abnormality
get.frequency.based.sizes
Function to size HPO nodes in plot based on frequency of occurrence in phenotypes
get.hpo.graph
Get HPO graph object
exclude.branch
Exclude terms descending from particular term from a character vector of terms
get.case.based.labels
Function to label HPO nodes in plot to indicate to which phenotypes each of the terms belong
get.ancestors
Get set of all ancestors of set of terms
get.shortened.names
Get human readable, shortened (where possible) HPO term names
get.mpo.to.hpo
Get MPO to HPO R-Object
hpo.terms
HPO Terms object (based on version 887 of the HPO)
get.significance.based.sizes
Function to size HPO nodes in plot with colours based on significance of seeing this many of each term in phenotypes
get.code.node.labels
Function to label HPO nodes in plot with just HPO code
get.no.borders
Function to border HPO nodes in plot with transparent borders
get.term.info.content
Get information content of each term in a set of phenotypes
setDimNames
setNames for arrays...
apply.term.filters
Apply a list of term filters to a given plotting context
get.simple.node.labels
Function to label HPO nodes in plot with just node description
get.pop.frequency.based.colours
Function to colour HPO nodes in plot with colours based on information content/frequency of terms with respect to population
prune.branch
Prune all terms descending from given term down to that term and ensure no degeneracy
get.frequency.based.labels
Function to label HPO nodes in plot based on frequency of occurrence in phenotypes
simpleCap
Capitalise words in character vector
get.term.pseudo.adjacency.matrix
Get an adjacency to MRCA matrix for set of HPO terms
get.case.based.colours
Function to set colours of HPO nodes in plot to distinguish terms belonging to different sets of phenotypes
get.informative.node.labels
Function to label HPO nodes in plot with node description and information content
n.most.frequent.terms
Select most frequently annotated terms from a set of phenotypes
get.frequency.based.colours
Function to colour HPO nodes in plot with colours based on frequency with which terms appear in phenotypes
get.term.frequencies
Get frequency of each term in a set of phenotypes
get.hpo.terms
Gets HPO R-Object
p.values.for.occurrence.of.term.in.group
Get p-values for observing at least as many of each term as have been in phenotypes given information content
get.case.term.matrix
Get a matrix with columns of hpo terms and rows of patients,
remove.uninformative.terms
Get a minimal set of terms which can be used to partition a set of phenotypes
calibrate.sizes
Function to scale sizes of terms between two given limits
get.grey.borders
Function to border HPO nodes in plot with grey borders
get.full.labels
Function to label HPO nodes in plot with full labels
get.ontology
Get R-Object representation of ontology from obo file
get.standard.sizes
Function to size HPO nodes in plot 0.75 inches across
clean.terms
Remove redundant/implied terms
mpo.to.hpo
Object containing data for mapping between MPO and HPO
swap.out.alt.ids
Remove alternate/deprecated HPO term IDs and swap for new ones
hpo.plot
Plot HPO graph object
intersection.with.branches
Intersect set of terms with branches of HPO
get.descendants
Get set of all descendants of single term
remove.links
Remove terms with exactly one parent and child from plot
remove.uninformative.for.plot
Remove uninformative terms (fitting plotting filter format)