Man pages for hpoPlot
Functions for Plotting HPO Terms

apply.term.filtersApply a list of term filters to a given plotting context
calibrate.sizesFunction to scale sizes of terms between two given limits
clean.termsRemove redundant/implied terms
exclude.branchExclude terms descending from particular term from a...
get.ancestorsGet set of all ancestors of set of terms
get.case.based.coloursFunction to set colours of HPO nodes in plot to distinguish...
get.case.based.labelsFunction to label HPO nodes in plot to indicate to which...
get.case.term.matrixGet a matrix with columns of hpo terms and rows of patients,
get.code.node.labelsFunction to label HPO nodes in plot with just HPO code
get.descendantsGet set of all descendants of single term
get.frequency.based.coloursFunction to colour HPO nodes in plot with colours based on...
get.frequency.based.labelsFunction to label HPO nodes in plot based on frequency of...
get.frequency.based.sizesFunction to size HPO nodes in plot based on frequency of...
get.full.labelsFunction to label HPO nodes in plot with full labels
get.hpo.graphGet HPO graph object
get.informative.node.labelsFunction to label HPO nodes in plot with node description and...
get.mpo.to.hpoGet MPO to HPO R-Object
get.node.friendly.long.namesSplit up the HPO term descriptions so they fit in nodes for...
get.ontologyGet R-Object representation of ontology from obo file
get.pop.frequency.based.coloursFunction to colour HPO nodes in plot with colours based on...
get.shortened.namesGet human readable, shortened (where possible) HPO term names
get.significance.based.sizesFunction to size HPO nodes in plot with colours based on...
get.simple.node.labelsFunction to label HPO nodes in plot with just node...
get.term.adjacency.matrixGet an adjacency for set of HPO terms
get.term.descendancy.matrixGet logical descendancy matrix for set of terms
get.term.frequenciesGet frequency of each term in a set of phenotypes
get.term.info.contentGet information content of each term in a set of phenotypes
get.term.pseudo.adjacency.matrixGet an adjacency to MRCA matrix for set of HPO terms
hpo.plotPlot HPO graph object
hpoPlot-packageFunctions for Plotting HPO Terms
hpo.termsHPO Terms object (based on version 887 of the HPO)
intersection.with.branchesIntersect set of terms with branches of HPO
mpo.termsMPO Terms object
mpo.to.hpoObject containing data for mapping between MPO and HPO
n.most.frequent.termsSelect most frequently annotated terms from a set of...
prune.branchPrune all terms descending from given term down to that term...
p.values.for.occurrence.of.term.in.groupGet p-values for observing at least as many of each term as...
remove.linksRemove terms with exactly one parent and child from plot
remove.non.pa.termsRemove terms not descending from phenotypic abnormality
remove.terms.with.less.than.n.occurrencesRemove terms with less than certain number of occurrences
remove.uninformative.for.plotRemove uninformative terms (fitting plotting filter format)
remove.uninformative.termsGet a minimal set of terms which can be used to partition a...
setDimNamessetNames for arrays...
simpleCapCapitalise words in character vector
swap.out.alt.idsRemove alternate/deprecated HPO term IDs and swap for new...
term.set.list.from.characterGet list of character vector of HPO terms, given character...
hpoPlot documentation built on May 29, 2017, 6:43 p.m.