Package hpoplot. R topics documented: December 14, 2015

Transcription

1 Type Package Title Functions for Plotting HPO Terms Version 2.4 Date Author Daniel Greene Maintainer Daniel Greene Package hpoplot December 14, 2015 Collection of functions for manipulating sets of HPO and plotting them with a various options. License GPL (>= 2) Depends R (>= 3.0.0) Imports methods, Rgraphviz, functional, magrittr Suggests knitr VignetteBuilder knitr RoxygenNote NeedsCompilation no Repository CRAN Date/Publication :07:27 R topics documented: apply.term.filters calibrate.sizes clean exclude.branch get.ancestors get.case.based.colours get.case.based.labels get.case.term.matrix get.code.node.labels get.descendants get.frequency.based.colours

2 2 apply.term.filters get.frequency.based.labels get.frequency.based.sizes get.full.labels get.hpo.graph get.informative.node.labels get.mpo.to.hpo get.node.friendly.long.names get.ontology get.pop.frequency.based.colours get.shortened.names get.significance.based.sizes get.simple.node.labels get.term.adjacency.matrix get.term.descendancy.matrix get.term.frequencies get.term.info.content get.term.pseudo.adjacency.matrix hpo.plot hpoplot intersection.with.branches mpo mpo.to.hpo n.most.frequent p.values.for.occurrence.of.term.in.group prune.branch remove.links remove.non.pa remove..with.less.than.n.occurrences remove.uninformative.for.plot remove.uninformative setdimnames simplecap swap.out.alt.ids term.set.list.from.character Index 33 apply.term.filters Apply a list of term filters to a given plotting context Apply a list of term filters to a given plotting context

3 calibrate.sizes 3 apply.term.filters(,, term.filters, starting. = NULL) List object with hpo.phenotypes slot for list of character vectors of term.filters List of term filtering functions starting. Character vector of HPO term codes to filter. Defaults to all in the hpo.phenotypes element of, if it is present Character vector of data() apply.term.filters(=, =list( hpo.phenotypes=list(case1="hp: ")), term.filters=list(remove.links)) calibrate.sizes Function to scale sizes of between two given limits Function to scale sizes of between two given limits calibrate.sizes(x, high, low) x high low Numeric vector of term relative sizes named by term Numeric vector of largest size Numeric vector of smallest size Numeric vector calibrate.sizes(c("hp: "=10, "HP: "=5), high=3, low=1)

4 4 exclude.branch clean. Remove redundant/implied Remove redundant/implied clean.(, ) data() clean.(, c("hp: ", "HP: ")) exclude.branch Exclude descending from particular term from a character vector of Exclude descending from particular term from a character vector of exclude.branch(, branch.root, ) branch.root HPO term whose descendants should be excluded Character vector of

5 get.ancestors 5 get.ancestors Get set of all ancestors of set of Get set of all ancestors of set of get.ancestors(, ) Character vector of all HPO which are an ancestor of at least one term in, including the themselves See Also link{get.descendants} data() get.ancestors(, c("hp: ", "HP: ")) get.case.based.colours Function to set colours of HPO nodes in plot to distinguish belonging to different sets of phenotypes Function to set colours of HPO nodes in plot to distinguish belonging to different sets of phenotypes get.case.based.colours(,, )

6 6 get.case.term.matrix List object with hpo.phenotypes slot for list of character vectors of Character vector of colours, named by term get.case.based.labels Function to label HPO nodes in plot to indicate to which phenotypes each of the belong Function to label HPO nodes in plot to indicate to which phenotypes each of the belong get.case.based.labels(,, ) List object with hpo.phenotypes slot for list of character vectors of Character vector of colours, named by term get.case.term.matrix Get a matrix with columns of hpo and rows of patients, Get a matrix with columns of hpo and rows of patients, get.case.term.matrix(hpo.phenotypes, columns = NULL)

7 get.code.node.labels 7 hpo.phenotypes List of character vectors of HPO. Result includes only which are explicitly present in the list items, so if you wish the result to include even which are implicitly present, lapply get.ancestors to the argument before passing it to this function columns Force result to have these exact columns, entering F for which aren t present Logical matrix - entry for a patient/hpo term = T if the patient has the term and F otherwise. get.case.term.matrix(list(patient1=c("hp: "))) get.code.node.labels Function to label HPO nodes in plot with just HPO code Function to label HPO nodes in plot with just HPO code get.code.node.labels(,, ) List object with hpo.phenotypes slot for list of character vectors of Character vector of labels, named by term

8 8 get.frequency.based.colours get.descendants Get set of all descendants of single term Get set of all descendants of single term get.descendants(, ancestor, remove.ancestor = FALSE) ancestor Character vector of length 1 - the HPO code of the term whose descendants you wish to retrieve remove.ancestor Boolean indicating whether to remove the given ancestor or not See Also Character vector of link{get.ancestors} data() get.descendants(, ancestor=c("hp: ")) get.frequency.based.colours Function to colour HPO nodes in plot with colours based on frequency with which appear in phenotypes Function to colour HPO nodes in plot with colours based on frequency with which appear in phenotypes get.frequency.based.colours(,,, colour.func = NULL)

9 get.frequency.based.labels 9 List object with hpo.phenotypes slot for list of character vectors of colour.func Function capable of returning a set of colours, given the number of colours it needs to return Character vector of colours, named by term get.frequency.based.labels Function to label HPO nodes in plot based on frequency of occurrence in phenotypes Function to label HPO nodes in plot based on frequency of occurrence in phenotypes get.frequency.based.labels(,, ) List object with hpo.phenotypes slot for list of character vectors of Character vector of labels, named by term

10 10 get.full.labels get.frequency.based.sizes Function to size HPO nodes in plot based on frequency of occurrence in phenotypes Function to size HPO nodes in plot based on frequency of occurrence in phenotypes get.frequency.based.sizes(,, ) List object with hpo.phenotypes slot for list of character vectors of Character vector of sizes, named by term get.full.labels Function to label HPO nodes in plot with full labels Function to label HPO nodes in plot with full labels get.full.labels(,, ) List object with hpo.phenotypes slot for list of character vectors of Character vector of labels, named by term

11 get.hpo.graph 11 get.hpo.graph Get HPO graph object Get HPO graph object get.hpo.graph(, = apply.term.filters( =, =, term.filters = list()), = NULL, colours = "white", labels = get.simple.node.labels, borders = "#FFFFFF00", sizes = 0.75, font.sizes = rep(30, length()), shapes = rep("circle", length()), nodeattrs = NULL, arrowattrs = list(color = "#000000")) List object with hpo.phenotypes slot for list of character vectors of colours labels borders sizes font.sizes shapes See Also nodeattrs arrowattrs grapham S4 object hpo.plot Function to set the colours of the HPO nodes in the graph based on the plotting context, or a character vector of colours Function to set the labels of the HPO nodes in the graph based on the plotting context, or a character vector of node labels Function to set the borders of the HPO nodes in the graph based on the plotting context, or a character vector of border colours Function to set the sizes of the HPO nodes in the graph based on the plotting context, or a numeric vector of node sizes Function to set the font sizes of the text to be placed in the HPO nodes in the graph based on the plotting context, or an integer vector of font sizes Function to set the shapes of the HPO nodes in the graph based on the plotting context, or a character vector of shape names (defaults to circle ) Pass nodeattrs directly to rgraphviz plotting function List of properties to set for arrows (note, these properties will be used for all arrow)

12 12 get.informative.node.labels data() phenotype.strings <- c( A="HP: ,HP: ,HP: ,HP: ,HP: ", B="HP: ,HP: ,HP: ,HP: ,HP: ", C="HP: ,HP: ,HP: ,HP: ,HP: ", D="HP: ,HP: ,HP: ,HP: ,HP: ", E="HP: ,HP: ,HP: ,HP: ,HP: " ) hpo.phenotypes <- term.set.list.from.character(phenotype.strings) get.hpo.graph( =, =list(hpo.phenotypes=hpo.phenotypes) ) get.informative.node.labels Function to label HPO nodes in plot with node description and information content Function to label HPO nodes in plot with node description and information content get.informative.node.labels(,, ) List object with hpo.phenotypes slot for list of character vectors of Character vector of labels, named by term

13 get.mpo.to.hpo 13 get.mpo.to.hpo Get MPO to HPO R-Object Get MPO to HPO R-Object get.mpo.to.hpo(, cross.species.file) cross.species.file cross species obo file, downloadable from website List of HPO per MPO term get.node.friendly.long.names Split up the HPO term descriptions so they fit in nodes for plot Split up the HPO term descriptions so they fit in nodes for plot get.node.friendly.long.names(, ) Character vector data() get.node.friendly.long.names(, c("hp: ", "HP: "))

14 14 get.pop.frequency.based.colours get.ontology Get R-Object representation of ontology from obo file Get R-Object representation of ontology from obo file get.ontology(file, qualifier = "HP") file qualifier File path of obo file Character vector - "HP" for HPO, "MP" for MPO, etc. R-Object (list) representing ontology get.pop.frequency.based.colours Function to colour HPO nodes in plot with colours based on information content/frequency of with respect to population Function to colour HPO nodes in plot with colours based on information content/frequency of with respect to population get.pop.frequency.based.colours(,,, colourpalette = colorramppalette(c("yellow", "Green", "#0099FF"))(10),.freq = if (is.null($frequency)) exp(-$information[]) else $frequency, max.colour.freq = max(.freq), min.colour.freq = min(.freq))

15 get.shortened.names 15 List object with hpo.phenotypes slot for list of character vectors of colourpalette Character vector of colours for the different information contents of the to be plotted, going from rare to common.freq Numeric vector of frequencies of in plot, named by term max.colour.freq Numeric value in [0, 1] giving the maximum frequency (to which the dullest color will be assigned) min.colour.freq Numeric value in [0, 1] giving the minimum frequency (to which the brightest color will be assigned) Character vector of colours, named by term get.shortened.names Get human readable, shortened (where possible) HPO term names Get human readable, shortened (where possible) HPO term names get.shortened.names(, ) Character vector data() get.shortened.names(, c("hp: ", "HP: "))

16 16 get.simple.node.labels 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 Function to size HPO nodes in plot with colours based on significance of seeing this many of each term in phenotypes get.significance.based.sizes(,, ) List object with hpo.phenotypes slot for list of character vectors of Character vector of sizes, named by term get.simple.node.labels Function to label HPO nodes in plot with just node description Function to label HPO nodes in plot with just node description get.simple.node.labels(,, ) List object with hpo.phenotypes slot for list of character vectors of Character vector of labels, named by term

17 get.term.adjacency.matrix 17 get.term.adjacency.matrix Get an adjacency for set of HPO Get an adjacency for set of HPO get.term.adjacency.matrix(, ) A logical matrix representing the directed adjacency matrix of based on DAG structure of HPO, whereby a TRUE entry signifies that the term corresponding to the column is a parent term of the term correspnding to the row. See Also get.term.pseudo.adjacency.matrix data() get.term.adjacency.matrix(, c("hp: ", "HP: ", "HP: ")) get.term.descendancy.matrix Get logical descendancy matrix for set of Get logical descendancy matrix for set of get.term.descendancy.matrix(, = NULL, rows =, cols = )

18 18 get.term.frequencies rows cols Rows for resultant matrix (defaults to ) Cols for resultant matrix (defaults to ) A logical descendancy matrix of by based on DAG structure of HPO, where by the row term is an ancestor of the column term if result[row.term,col.term] == TRUE data() get.term.descendancy.matrix(, c("hp: ", "HP: ")) get.term.frequencies Get frequency of each term in a set of phenotypes Get frequency of each term in a set of phenotypes get.term.frequencies(, hpo.phenotypes, patch.missing = FALSE) hpo.phenotypes List of HPO term character vectors patch.missing Logical indicating whether to include all HPO even if they re not present in the hpo.phenotypes as if they had occurred once Numeric vector of information contents, named by corresponding HPO. Takes into account ancestors, in the sense that all ancestor implied by the phenotypes are considered on See Also get.term.info.content data() get.term.frequencies(, list("hp: "))

19 get.term.info.content 19 get.term.info.content Get information content of each term in a set of phenotypes Get information content of each term in a set of phenotypes get.term.info.content(, hpo.phenotypes, patch.missing = FALSE) hpo.phenotypes List of HPO term character vectors patch.missing Logical indicating whether to include all HPO even if they re not present in the hpo.phenotypes as if they had occurred once Numeric vector of information contents, named by corresponding HPO. Takes into account ancestors, in the sense that all ancestor implied by the phenotypes are considered on data() get.term.info.content(, list("hp: ")) get.term.pseudo.adjacency.matrix Get an adjacency to MRCA matrix for set of HPO Get an adjacency to MRCA matrix for set of HPO get.term.pseudo.adjacency.matrix(, )

20 20 hpo.plot A logical matrix represenging the directed adjacency matrix of based on DAG structure of HPO, whereby a TRUE entry signifies the term correspnding to the column is MRCA of the row term in See Also get.term.adjacency.matrix data() get.term.pseudo.adjacency.matrix(, c("hp: ", "HP: ", "HP: ")) hpo.plot Plot HPO graph object Plot HPO graph object hpo.plot(, = apply.term.filters( =, =, term.filters = list()), = NULL, hpo.phenotypes = NULL, term.frequencies = NULL, colours = "cyan", labels = get.simple.node.labels, borders = "#FFFFFF00", sizes = 0.75, font.sizes = rep(30, length()), shapes = rep("circle", length()), nodeattrs = NULL, arrowattrs = list(color = "#000000"),...) List object with hpo.phenotypes slot for list of character vectors of hpo.phenotypes List of HPO term character vectors term.frequencies Numeric vector of population frequencies of (named by term codes) colours labels borders Function to set the colours of the HPO nodes in the graph based on the plotting context, or a character vector of colours Function to set the labels of the HPO nodes in the graph based on the plotting context, or a character vector of node labels Function to set the borders of the HPO nodes in the graph based on the plotting context, or a character vector of border colours

21 21 sizes font.sizes shapes nodeattrs arrowattrs Function to set the sizes of the HPO nodes in the graph based on the plotting context, or a numeric vector of node sizes Function to set the font sizes of the text to be placed in the HPO nodes in the graph based on the plotting context, or an integer vector of font sizes Function to set the shapes of the HPO nodes in the graph based on the plotting context, or a character vector of shape names (defaults to circle ) Pass nodeattrs directly to rgraphviz plotting function List of properties to set for arrows (note, these properties will be used for all arrow)... Extra arguments to pass to plot Plots graph See Also get.hpo.graph data() hpo.plot( =, =get.ancestors(, c("hp: ","hp: ","hp: ","hp: ","hp: ")) ) HPO Terms object (based on version 887 of the HPO) Object comprising list of properties of the HPO, indexed by term ID Format List of indices containing metadata and structure of HPO

22 22 hpoplot hpoplot Functions for Plotting HPO Terms Details Functions for performaing operations on sets of HPO (character vectors of HPO term IDs) in the context of the HPO structure, and plotting them with a various options

23 intersection.with.branches 23 Package: hpoplot Type: Package Version: 2.3 Date: License: GPL (>= 2) The key function is hpo.plot, which plots a set of phenotype given their HPO IDs and their ontological relations given by the HPO. Author(s) Daniel Greene <dg333@cam.ac.uk> Maintainer: Daniel Greene <dg333@cam.ac.uk> References The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data, Nucl. Acids Res. (1 January 2014) 42 (D1): D966-D974 doi: /nar/gkt1026 Westbury, S. K. et al. (2015). Human Phenotype Ontology annotation and cluster analysis to un- ravel genetic defects in 707 cases with unexplained bleeding and platelet disorders. Genome Medicine. 7 (2015) intersection.with.branches Intersect set of with branches of HPO Intersect set of with branches of HPO intersection.with.branches(, branch.roots, ) branch.roots Character vector of roots of branches you wish to intersect with Character vector of

24 24 n.most.frequent. data() intersection.with.branches(, "HP: ", c("hp: ", "HP: ")) mpo. MPO Terms object Object comprising list of properties of the MPO, indexed by term ID Format List of indices containing metadata and structure of MPO mpo.to.hpo Object containing data for mapping between MPO and HPO Format List containing cross-species ontology (MPO to HPO) information - character vectors of HPO indexed by associated MPO term IDs List of HPO per MPO term n.most.frequent. Select most frequently annotated from a set of phenotypes Select most frequently annotated from a set of phenotypes n.most.frequent.(,,, n) List object with hpo.phenotypes slot for list of character vectors of n Integer

25 p.values.for.occurrence.of.term.in.group 25 Character vector of length at most n See Also remove..with.less.than.n.occurrences, remove.uninformative.for.plot data() n.most.frequent.(, c("hp: "), list(hpo.phenotypes=list("hp: ", "HP: ")), n=2) 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 p-values for observing at least as many of each term as have been in phenotypes given information content p.values.for.occurrence.of.term.in.group(, hpo.phenotypes,.freq) hpo.phenotypes List of HPO term character vectors.freq Numeric vector of population frequencies of Numeric vector of log p-values named by correspnding term

26 26 remove.links prune.branch Prune all descending from given term down to that term and ensure no degeneracy Prune all descending from given term down to that term and ensure no degeneracy prune.branch(, prune.to.point, ) prune.to.point HPO term which can be included, but whose descendants should be excluded Character vector of remove.links Remove with exactly one parent and child from plot Remove with exactly one parent and child from plot remove.links(,, = NULL) List object with hpo.phenotypes slot for list of character vectors of Character vector

27 remove.non.pa. 27 See Also remove..with.less.than.n.occurrences, n.most.frequent. data() remove.links(, c("hp: "), list(hpo.phenotypes=list("hp: ", "HP: "))) remove.non.pa. Remove not descending from phenotypic abnormality Remove not descending from phenotypic abnormality remove.non.pa.(,, ) List object with hpo.phenotypes slot for list of character vectors of Character vector See Also remove..with.less.than.n.occurrences, n.most.frequent.

28 28 remove.uninformative.for.plot remove..with.less.than.n.occurrences Remove with less than certain number of occurrences Remove with less than certain number of occurrences remove..with.less.than.n.occurrences(,,, n) List object with hpo.phenotypes slot for list of character vectors of n See Also Character vector Integer n.most.frequent., remove.uninformative.for.plot data() remove..with.less.than.n.occurrences(, c("hp: "), list(hpo.phenotypes=list("hp: ", "HP: ")), 2) remove.uninformative.for.plot Remove uninformative (fitting plotting filter format) Remove uninformative (fitting plotting filter format) remove.uninformative.for.plot(, = get.ancestors(, unlist($hpo.phenotypes)), )

29 remove.uninformative. 29 List object with hpo.phenotypes slot for list of character vectors of See Also Character vector remove..with.less.than.n.occurrences, n.most.frequent. data() remove.uninformative.for.plot(, c("hp: "), list(hpo.phenotypes=list("hp: ", "HP: "))) remove.uninformative. Get a minimal set of which can be used to partition a set of phenotypes Get a minimal set of which can be used to partition a set of phenotypes remove.uninformative.(, hpo.phenotypes) hpo.phenotypes List of HPO term character vectors Character vector of set of, excluding for which the presence of their descendants all partition the set of in the same way data() remove.uninformative.(, list(patient1=c("hp: ")))

30 30 simplecap setdimnames setnames for arrays... setnames for arrays... setdimnames(array.object, list.of.dimension.names) array.object Array list.of.dimension.names List of character vectors with which to name each dimension of the array Named array setdimnames(matrix(1:4,2,2), list(c("cat", "Dog"), c("name", "Weight"))) simplecap Capitalise words in character vector Capitalise words in character vector simplecap(x) x Character vector Character vector simplecap(c("a simple test", "Another-test"))

31 swap.out.alt.ids 31 swap.out.alt.ids Remove alternate/deprecated HPO term IDs and swap for new ones Remove alternate/deprecated HPO term IDs and swap for new ones swap.out.alt.ids(,, remove.dead = FALSE) remove.dead Boolean to indicate whether to strip out which can t be found in the given database argument A directed adjacency matrix of based on DAG structure of HPO, whereby each term is considered adjacent to it s MRCA in data() swap.out.alt.ids(, c("hp: ")) term.set.list.from.character Get list of character vector of HPO, given character vector of comma separated Get list of character vector of HPO, given character vector of comma separated term.set.list.from.character(character.vector) character.vector Character vector of comma separated

32 32 term.set.list.from.character List of character vectors of HPO term.set.list.from.character(c("hp: ", "HP: "))

33 Index Topic HPO hpoplot, 22 apply.term.filters, 2 calibrate.sizes, 3 clean., 4 exclude.branch, 4 get.ancestors, 5, 7 get.case.based.colours, 5 get.case.based.labels, 6 get.case.term.matrix, 6 get.code.node.labels, 7 get.descendants, 8 get.frequency.based.colours, 8 get.frequency.based.labels, 9 get.frequency.based.sizes, 10 get.full.labels, 10 get.hpo.graph, 11, 21 get.informative.node.labels, 12 get.mpo.to.hpo, 13 get.node.friendly.long.names, 13 get.ontology, 14 get.pop.frequency.based.colours, 14 get.shortened.names, 15 get.significance.based.sizes, 16 get.simple.node.labels, 16 get.term.adjacency.matrix, 17, 20 get.term.descendancy.matrix, 17 get.term.frequencies, 18 get.term.info.content, 18, 19 get.term.pseudo.adjacency.matrix, 17, 19 mpo., 24 mpo.to.hpo, 24 n.most.frequent., 24, p.values.for.occurrence.of.term.in.group, 25 prune.branch, 26 remove.links, 26 remove.non.pa., 27 remove..with.less.than.n.occurrences, 25, 27, 28, 29 remove.uninformative.for.plot, 25, 28, 28 remove.uninformative., 29 setdimnames, 30 simplecap, 30 swap.out.alt.ids, 31 term.set.list.from.character, 31 hpo.plot, 11, 20, 23, 21 hpoplot, 22 intersection.with.branches, 23 33