vignettes/HPOExplorer.Rmd
HPOExplorer.RmdWithin R:
if (!require("remotes")) install.packages("remotes")
if (!require("HPOExplorer")) remotes::install_github("neurogenomics/HPOExplorer")The HPOExplorer package provides useful functions for
working with the Human Phenotype
Ontology (HPO). The main HPO ontology object comes with the simona
R package.
This tutorial will focus on creating an interactive network plot of a subset of the HPO, where disease descriptions and results from your analysis appear in a hover box when a specific phenotype is selected from the graph.
hpo <- get_hpo()The figure we are going to create is a bit arbitrary, but it should outline the main features of the package. First we are going to get a subset of HPO terms to plot. We will select phenotypes that are descendants of “Neurodevelopmental delay”.
ancestor <- "Neurodevelopmental delay"To create the network object we need a dataframe of the selected phenotypes with columns for associated parameters. We will be able to map these parameters onto the colour of the nodes in the figure. We can also use them to subset the selected phenotypes further.
Typically, these parameters would be results from an analysis you have done. For example, you may have p values associated with each phenotype and you might want to only show phenotypes where p<0.05, or use them to colour the nodes, or have the p values displayed in the hover box.
For this example we will have to make up a parameter for demonstration purposes. We are going to divide ontology level of the phenotypes by the number of associated genes. We will also include the ontology level its self and the disease description.
HPOExplorer has some useful functions for obtaining the
ontology level of terms. Ontology level describes the number of
generations of descendants vertically below a term (note that this is
not the same as the raw number of descendants which is also capturing
the horizontal spread of branching off terms). For example “Phenotypic
abnormality” is high up in the HPO and all other disease phenotypes are
descendants of it. It is at ontology level 13. A term with no
descendants is at ontology level 0.
phenos <- make_phenos_dataframe(hpo = hpo,
ancestor = ancestor)Then we can make the plot with make_network_plot. Again
you need to give the column name for the variable you want mapped to
colour in the colour_var argument. We also need to provide
a nice label for this column in colour_label. This will be
used for the figure legend.
The colour_var argument is where you choose the column
name from the phenos dataframe which you want to be mapped
to the colour of the nodes. In this case we created the family arbitrary
variable of ontology level to number of associated genes ratio and its
column name is ontLvl_geneCount_ratio.
plt <- make_network_plot(phenos = phenos,
colour_var = "ontLvl_geneCount_ratio")
methods::show(plt)## $data
## x y name short_id namespace
## 5 0.15279342 0.87311568 HP:0002194 HP:0002194 human_phenotype
## 6 0.15279342 0.87311568 HP:0002194 HP:0002194 human_phenotype
## 7 0.15279342 0.87311568 HP:0002194 HP:0002194 human_phenotype
## 8 0.15279342 0.87311568 HP:0002194 HP:0002194 human_phenotype
## 9 0.15279342 0.87311568 HP:0002194 HP:0002194 human_phenotype
## 12 0.39227536 0.73673405 HP:0001270 HP:0001270 human_phenotype
## 13 0.39227536 0.73673405 HP:0001270 HP:0001270 human_phenotype
## 14 0.39227536 0.73673405 HP:0001270 HP:0001270 human_phenotype
## 18 0.55999140 0.17686512 HP:0002474 HP:0002474 human_phenotype
## 19 0.61722785 0.56360905 HP:0012758 HP:0012758 human_phenotype
## 20 0.61722785 0.56360905 HP:0012758 HP:0012758 human_phenotype
## 21 0.61722785 0.56360905 HP:0012758 HP:0012758 human_phenotype
## 22 0.61722785 0.56360905 HP:0012758 HP:0012758 human_phenotype
## 23 0.66333947 0.31086941 HP:0000750 HP:0000750 human_phenotype
## 24 0.66333947 0.31086941 HP:0000750 HP:0000750 human_phenotype
## 25 0.66333947 0.31086941 HP:0000750 HP:0000750 human_phenotype
## 26 0.76452271 0.13023709 HP:0010863 HP:0010863 human_phenotype
## 27 0.76452271 0.13023709 HP:0010863 HP:0010863 human_phenotype
## 30 0.84715080 0.66590572 HP:0001263 HP:0001263 human_phenotype
## 31 0.84715080 0.66590572 HP:0001263 HP:0001263 human_phenotype
## 32 0.84715080 0.66590572 HP:0001263 HP:0001263 human_phenotype
## 33 0.84715080 0.66590572 HP:0001263 HP:0001263 human_phenotype
## 1 0.66333947 0.31086941 HP:0000750 HP:0000750 human_phenotype
## 2 0.84715080 0.66590572 HP:0001263 HP:0001263 human_phenotype
## 3 0.39227536 0.73673405 HP:0001270 HP:0001270 human_phenotype
## 4 0.76589549 0.26904135 HP:0001344 HP:0001344 human_phenotype
## 51 0.15279342 0.87311568 HP:0002194 HP:0002194 human_phenotype
## 61 0.55999140 0.17686512 HP:0002474 HP:0002474 human_phenotype
## 71 0.48312691 0.06947758 HP:0006863 HP:0006863 human_phenotype
## 81 0.32825088 0.79947172 HP:0010862 HP:0010862 human_phenotype
## 91 0.76452271 0.13023709 HP:0010863 HP:0010863 human_phenotype
## 10 0.96226695 0.60384804 HP:0011342 HP:0011342 human_phenotype
## 11 0.86437797 0.78577699 HP:0011343 HP:0011343 human_phenotype
## 121 0.95789216 0.76088017 HP:0011344 HP:0011344 human_phenotype
## 131 0.87570712 0.04684868 HP:0011351 HP:0011351 human_phenotype
## 141 0.77583924 0.00000000 HP:0011352 HP:0011352 human_phenotype
## 15 0.53625823 0.50634410 HP:0012434 HP:0012434 human_phenotype
## 16 1.00000000 0.68518161 HP:0012736 HP:0012736 human_phenotype
## 17 0.61722785 0.56360905 HP:0012758 HP:0012758 human_phenotype
## 181 0.04887418 0.79347351 HP:0025335 HP:0025335 human_phenotype
## 191 0.08244327 1.00000000 HP:0025336 HP:0025336 human_phenotype
## 201 0.17742047 0.99777738 HP:0031936 HP:0031936 human_phenotype
## 211 0.45188343 0.83279170 HP:0032988 HP:0032988 human_phenotype
## 221 0.01618939 0.94608485 HP:0032989 HP:0032989 human_phenotype
## 231 0.00000000 0.86623779 HP:0033128 HP:0033128 human_phenotype
## definition
## 5 A type of motor delay characterized by a delay in acquiring the ability to control the large muscles of the body for walking, running, sitting, and crawling.
## 6 A type of motor delay characterized by a delay in acquiring the ability to control the large muscles of the body for walking, running, sitting, and crawling.
## 7 A type of motor delay characterized by a delay in acquiring the ability to control the large muscles of the body for walking, running, sitting, and crawling.
## 8 A type of motor delay characterized by a delay in acquiring the ability to control the large muscles of the body for walking, running, sitting, and crawling.
## 9 A type of motor delay characterized by a delay in acquiring the ability to control the large muscles of the body for walking, running, sitting, and crawling.
## 12 A type of Developmental delay characterized by a delay in acquiring motor skills.
## 13 A type of Developmental delay characterized by a delay in acquiring motor skills.
## 14 A type of Developmental delay characterized by a delay in acquiring motor skills.
## 18 A delay in the acquisition of the ability to use language to communicate needs, wishes, or thoughts.
## 19 Neurodevelopmental delay (NDD) refers to delays in the maturation of the brain and central nervous system; infants and young children with NDD may experience delays in the development of one or more skills including gross motor abilities, fine-motor coordination, language abilities and ability to solve increasingly complex problems.
## 20 Neurodevelopmental delay (NDD) refers to delays in the maturation of the brain and central nervous system; infants and young children with NDD may experience delays in the development of one or more skills including gross motor abilities, fine-motor coordination, language abilities and ability to solve increasingly complex problems.
## 21 Neurodevelopmental delay (NDD) refers to delays in the maturation of the brain and central nervous system; infants and young children with NDD may experience delays in the development of one or more skills including gross motor abilities, fine-motor coordination, language abilities and ability to solve increasingly complex problems.
## 22 Neurodevelopmental delay (NDD) refers to delays in the maturation of the brain and central nervous system; infants and young children with NDD may experience delays in the development of one or more skills including gross motor abilities, fine-motor coordination, language abilities and ability to solve increasingly complex problems.
## 23 A degree of language development that is significantly below the norm for a child of a specified age.
## 24 A degree of language development that is significantly below the norm for a child of a specified age.
## 25 A degree of language development that is significantly below the norm for a child of a specified age.
## 26 A delay in the acquisition of the ability to understand the speech of others.
## 27 A delay in the acquisition of the ability to understand the speech of others.
## 30 A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age.
## 31 A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age.
## 32 A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age.
## 33 A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age.
## 1 A degree of language development that is significantly below the norm for a child of a specified age.
## 2 A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age.
## 3 A type of Developmental delay characterized by a delay in acquiring motor skills.
## 4 Complete lack of development of speech and language abilities.
## 51 A type of motor delay characterized by a delay in acquiring the ability to control the large muscles of the body for walking, running, sitting, and crawling.
## 61 A delay in the acquisition of the ability to use language to communicate needs, wishes, or thoughts.
## 71 A severe delay in the acquisition of the ability to use language to communicate needs, wishes, or thoughts.
## 81 A type of motor delay characterized by a delay in acquiring the ability to control the fingers and hands.
## 91 A delay in the acquisition of the ability to understand the speech of others.
## 10 A mild delay in the achievement of motor or mental milestones in the domains of development of a child.
## 11 A moderate delay in the achievement of motor or mental milestones in the domains of development of a child.
## 121 A severe delay in the achievement of motor or mental milestones in the domains of development of a child.
## 131 A moderate delay in the acquisition of the ability to understand the speech of others.
## 141 A severe delay in the acquisition of the ability to understand the speech of others.
## 15 A failure to meet one or more age-related milestones of social behavior.
## 16 A profound delay in the achievement of motor or mental milestones in the domains of development of a child.
## 17 Neurodevelopmental delay (NDD) refers to delays in the maturation of the brain and central nervous system; infants and young children with NDD may experience delays in the development of one or more skills including gross motor abilities, fine-motor coordination, language abilities and ability to solve increasingly complex problems.
## 181 A failure to achieve the ability to stand up at an appropriate developmental stage. Most children begin to walk alone at 11 to 15 months of age. On average, children can stand while holding on at the age of 9 to 10 months, can pull up to stand and walk with one hand being held at 12 months, and can stand alone and walk well at 18 months.
## 191 A failure to achieve the ability to sit at an appropriate developmental stage. Most children sit with support at 6 months of age and sit steadily without support at 9 months of age.
## 201 A failure to achieve the ability to walk at an appropriate developmental stage. Most children learn to walk in a series of stages, and learn to walk short distances independently between 12 and 15 months.
## 211 The Premie-Neuro and the Dubowitz Neurological Examination score head lag in the same manner. Scoring for both is as follows: 0 = head drops and stays back, 1 = tries to lift head but drops it back, 2 = able to lift head slightly, 3 = lifts head in line with body, and 4 = head in front of body. This term applies if head lag persists beyond an expected age at a level of 0 or 1. Persistent head lag beyond age 4 mo has been linked to poor outcomes.
## 221 Delayed achievement of the ability to roll front to back and back to front.
## 231 A failure to achieve the ability to crawl at an appropriate developmental stage. Normal infant motor development is marked by a series of postural milestones including learning to crawl on hands and knees between the ages of 6 and 10 months.
## IC depth n_children n_ancestors n_parents n_offspring
## 5 7.881560 7 6 7 1 6
## 6 7.881560 7 6 7 1 6
## 7 7.881560 7 6 7 1 6
## 8 7.881560 7 6 7 1 6
## 9 7.881560 7 6 7 1 6
## 12 7.524885 6 3 6 1 9
## 13 7.524885 6 3 6 1 9
## 14 7.524885 6 3 6 1 9
## 18 8.441176 8 3 11 1 3
## 19 6.460174 5 4 5 1 28
## 20 6.460174 5 4 5 1 28
## 21 6.460174 5 4 5 1 28
## 22 6.460174 5 4 5 1 28
## 23 7.429575 7 3 10 3 10
## 24 7.429575 7 3 10 3 10
## 25 7.429575 7 3 10 3 10
## 26 8.218032 8 4 11 1 4
## 27 8.218032 8 4 11 1 4
## 30 8.218032 6 4 6 1 4
## 31 8.218032 6 4 6 1 4
## 32 8.218032 6 4 6 1 4
## 33 8.218032 6 4 6 1 4
## 1 7.429575 7 3 10 3 10
## 2 8.218032 6 4 6 1 4
## 3 7.524885 6 3 6 1 9
## 4 9.827470 8 0 11 2 0
## 51 7.881560 7 6 7 1 6
## 61 8.441176 8 3 11 1 3
## 71 9.827470 9 0 12 1 0
## 81 9.827470 7 0 7 1 0
## 91 8.218032 8 4 11 1 4
## 10 9.827470 7 0 7 1 0
## 11 9.827470 7 0 7 1 0
## 121 9.827470 7 0 7 1 0
## 131 9.827470 9 0 12 1 0
## 141 9.827470 9 0 12 1 0
## 15 9.134323 7 1 9 2 1
## 16 9.827470 7 0 7 1 0
## 17 6.460174 5 4 5 1 28
## 181 9.827470 8 0 8 1 0
## 191 9.827470 8 0 8 1 0
## 201 9.827470 8 0 8 1 0
## 211 9.827470 7 0 7 1 0
## 221 9.827470 8 0 8 1 0
## 231 9.827470 8 0 8 1 0
## n_connected_leaves ancestor ancestor_name n_edges
## 5 6 HP:0000707 Abnormality of the nervous system 1
## 6 6 HP:0000707 Abnormality of the nervous system 1
## 7 6 HP:0000707 Abnormality of the nervous system 1
## 8 6 HP:0000707 Abnormality of the nervous system 1
## 9 6 HP:0000707 Abnormality of the nervous system 1
## 12 8 HP:0000707 Abnormality of the nervous system 1
## 13 8 HP:0000707 Abnormality of the nervous system 1
## 14 8 HP:0000707 Abnormality of the nervous system 1
## 18 3 HP:0000707 Abnormality of the nervous system 1
## 19 21 HP:0000707 Abnormality of the nervous system 1
## 20 21 HP:0000707 Abnormality of the nervous system 1
## 21 21 HP:0000707 Abnormality of the nervous system 1
## 22 21 HP:0000707 Abnormality of the nervous system 1
## 23 8 HP:0000707 Abnormality of the nervous system 3
## 24 8 HP:0000707 Abnormality of the nervous system 3
## 25 8 HP:0000707 Abnormality of the nervous system 3
## 26 4 HP:0000707 Abnormality of the nervous system 1
## 27 4 HP:0000707 Abnormality of the nervous system 1
## 30 4 HP:0000707 Abnormality of the nervous system 1
## 31 4 HP:0000707 Abnormality of the nervous system 1
## 32 4 HP:0000707 Abnormality of the nervous system 1
## 33 4 HP:0000707 Abnormality of the nervous system 1
## 1 8 HP:0000707 Abnormality of the nervous system 3
## 2 4 HP:0000707 Abnormality of the nervous system 1
## 3 8 HP:0000707 Abnormality of the nervous system 1
## 4 1 HP:0000707 Abnormality of the nervous system 2
## 51 6 HP:0000707 Abnormality of the nervous system 1
## 61 3 HP:0000707 Abnormality of the nervous system 1
## 71 1 HP:0000707 Abnormality of the nervous system 1
## 81 1 HP:0000707 Abnormality of the nervous system 1
## 91 4 HP:0000707 Abnormality of the nervous system 1
## 10 1 HP:0000707 Abnormality of the nervous system 1
## 11 1 HP:0000707 Abnormality of the nervous system 1
## 121 1 HP:0000707 Abnormality of the nervous system 1
## 131 1 HP:0000707 Abnormality of the nervous system 1
## 141 1 HP:0000707 Abnormality of the nervous system 1
## 15 1 HP:0000707 Abnormality of the nervous system 2
## 16 1 HP:0000707 Abnormality of the nervous system 1
## 17 21 HP:0000707 Abnormality of the nervous system 1
## 181 1 HP:0000707 Abnormality of the nervous system 1
## 191 1 HP:0000707 Abnormality of the nervous system 1
## 201 1 HP:0000707 Abnormality of the nervous system 1
## 211 1 HP:0000707 Abnormality of the nervous system 1
## 221 1 HP:0000707 Abnormality of the nervous system 1
## 231 1 HP:0000707 Abnormality of the nervous system 1
## ontLvl hpo_name
## 5 7 Delayed gross motor development
## 6 7 Delayed gross motor development
## 7 7 Delayed gross motor development
## 8 7 Delayed gross motor development
## 9 7 Delayed gross motor development
## 12 6 Motor delay
## 13 6 Motor delay
## 14 6 Motor delay
## 18 8 Expressive language delay
## 19 5 Neurodevelopmental delay
## 20 5 Neurodevelopmental delay
## 21 5 Neurodevelopmental delay
## 22 5 Neurodevelopmental delay
## 23 7 Delayed speech and language development
## 24 7 Delayed speech and language development
## 25 7 Delayed speech and language development
## 26 8 Receptive language delay
## 27 8 Receptive language delay
## 30 6 Global developmental delay
## 31 6 Global developmental delay
## 32 6 Global developmental delay
## 33 6 Global developmental delay
## 1 7 Delayed speech and language development
## 2 6 Global developmental delay
## 3 6 Motor delay
## 4 8 Absent speech
## 51 7 Delayed gross motor development
## 61 8 Expressive language delay
## 71 9 Severe expressive language delay
## 81 7 Delayed fine motor development
## 91 8 Receptive language delay
## 10 7 Mild global developmental delay
## 11 7 Moderate global developmental delay
## 121 7 Severe global developmental delay
## 131 9 Moderate receptive language delay
## 141 9 Severe receptive language delay
## 15 7 Delayed early-childhood social milestone development
## 16 7 Profound global developmental delay
## 17 5 Neurodevelopmental delay
## 181 8 Delayed ability to stand
## 191 8 Delayed ability to sit
## 201 8 Delayed ability to walk
## 211 7 Persistent head lag
## 221 8 Delayed ability to roll over
## 231 8 Delayed ability to crawl
## ontLvl_geneCount_ratio xend yend
## 5 0.014957265 0.06871704 0.80868078
## 6 0.014957265 0.09456575 0.97813575
## 7 0.014957265 0.17257533 0.97325138
## 8 0.014957265 0.03824059 0.93430586
## 9 0.014957265 0.02497471 0.86736201
## 12 0.006036217 0.17451766 0.86074403
## 13 0.006036217 0.34610708 0.78197441
## 14 0.006036217 0.43870158 0.81154932
## 18 0.142857143 0.49767780 0.08980666
## 19 0.002025111 0.65885236 0.33546343
## 20 0.002025111 0.82430952 0.65574325
## 21 0.002025111 0.41208736 0.72148660
## 22 0.002025111 0.55666936 0.52077967
## 23 0.006375228 0.74274680 0.27848267
## 24 0.006375228 0.57525902 0.19666158
## 25 0.006375228 0.75230495 0.15204824
## 26 0.533333333 0.85570713 0.06184869
## 27 0.533333333 0.77367510 0.02490615
## 30 0.003076923 0.94026092 0.61571121
## 31 0.003076923 0.86082166 0.76103123
## 32 0.003076923 0.93891526 0.74460513
## 33 0.003076923 0.97519646 0.68205362
## 1 0.006375228 0.66333947 0.31086941
## 2 0.003076923 0.84715080 0.66590572
## 3 0.006036217 0.39227536 0.73673405
## 4 0.018823529 0.76589549 0.26904135
## 51 0.014957265 0.15279342 0.87311568
## 61 0.142857143 0.55999140 0.17686512
## 71 0.750000000 0.48312691 0.06947758
## 81 0.145833333 0.32825088 0.79947172
## 91 0.533333333 0.76452271 0.13023709
## 10 0.085365854 0.96226695 0.60384804
## 11 0.259259259 0.86437797 0.78577699
## 121 0.030172414 0.95789216 0.76088017
## 131 3.000000000 0.87570712 0.04684868
## 141 4.500000000 0.77583924 0.00000000
## 15 0.333333333 0.53625823 0.50634410
## 16 0.098591549 1.00000000 0.68518161
## 17 0.002025111 0.61722785 0.56360905
## 181 0.470588235 0.04887418 0.79347351
## 191 0.093023256 0.08244327 1.00000000
## 201 0.027491409 0.17742047 0.99777738
## 211 0.233333333 0.45188343 0.83279170
## 221 0.500000000 0.01618939 0.94608485
## 231 1.000000000 0.00000000 0.86623779
##
## $plot
utils::sessionInfo()## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] HPOExplorer_1.0.2
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 jsonlite_1.8.8
## [3] shape_1.4.6.1 magrittr_2.0.3
## [5] farver_2.1.2 rmarkdown_2.27
## [7] GlobalOptions_0.1.2 fs_1.6.4
## [9] ragg_1.3.2 vctrs_0.6.5
## [11] memoise_2.0.1 ggtree_3.13.0
## [13] rstatix_0.7.2 htmltools_0.5.8.1
## [15] broom_1.0.6 gridGraphics_0.5-1
## [17] sass_0.4.9 bslib_0.7.0
## [19] htmlwidgets_1.6.4 desc_1.4.3
## [21] httr2_1.0.1 plotly_4.10.4
## [23] cachem_1.1.0 igraph_2.0.3
## [25] mime_0.12 lifecycle_1.0.4
## [27] ggnetwork_0.5.13 iterators_1.0.14
## [29] pkgconfig_2.0.3 Matrix_1.7-0
## [31] R6_2.5.1 fastmap_1.2.0
## [33] shiny_1.8.1.1 clue_0.3-65
## [35] digest_0.6.35 aplot_0.2.2
## [37] colorspace_2.1-0 patchwork_1.2.0
## [39] S4Vectors_0.43.0 grr_0.9.5
## [41] crosstalk_1.2.1 textshaping_0.3.7
## [43] ggpubr_0.6.0 labeling_0.4.3
## [45] fansi_1.0.6 httr_1.4.7
## [47] KGExplorer_0.99.01 abind_1.4-5
## [49] compiler_4.4.0 withr_3.0.0
## [51] doParallel_1.0.17 backports_1.4.1
## [53] BiocParallel_1.39.0 orthogene_1.11.0
## [55] carData_3.0-5 homologene_1.4.68.19.3.27
## [57] maps_3.4.2 ggsignif_0.6.4
## [59] rappdirs_0.3.3 rjson_0.2.21
## [61] scatterplot3d_0.3-44 tools_4.4.0
## [63] ape_5.8 httpuv_1.6.15
## [65] glue_1.7.0 rols_3.1.0
## [67] nlme_3.1-164 promises_1.3.0
## [69] grid_4.4.0 cluster_2.1.6
## [71] generics_0.1.3 gtable_0.3.5
## [73] tidyr_1.3.1 data.table_1.15.4
## [75] tidygraph_1.3.1 xml2_1.3.6
## [77] car_3.1-2 utf8_1.2.4
## [79] BiocGenerics_0.51.0 foreach_1.5.2
## [81] pillar_1.9.0 stringr_1.5.1
## [83] yulab.utils_0.1.4 babelgene_22.9
## [85] pals_1.9 later_1.3.2
## [87] circlize_0.4.16 dplyr_1.1.4
## [89] treeio_1.29.0 lattice_0.22-6
## [91] tidyselect_1.2.1 ComplexHeatmap_2.21.0
## [93] knitr_1.46 IRanges_2.39.0
## [95] stats4_4.4.0 xfun_0.44
## [97] Biobase_2.65.0 matrixStats_1.3.0
## [99] stringi_1.8.4 lazyeval_0.2.2
## [101] ggfun_0.1.4 yaml_2.3.8
## [103] evaluate_0.23 codetools_0.2-20
## [105] tibble_3.2.1 ggplotify_0.1.2
## [107] Polychrome_1.5.1 cli_3.6.2
## [109] xtable_1.8-4 systemfonts_1.1.0
## [111] munsell_0.5.1 jquerylib_0.1.4
## [113] dichromat_2.0-0.1 Rcpp_1.0.12
## [115] mapproj_1.2.11 gprofiler2_0.2.3
## [117] png_0.1-8 parallel_4.4.0
## [119] simona_1.3.0 pkgdown_2.0.9
## [121] ggplot2_3.5.1 viridisLite_0.4.2
## [123] tidytree_0.4.6 scales_1.3.0
## [125] purrr_1.0.2 crayon_1.5.2
## [127] GetoptLong_1.0.5 rlang_1.1.3
## [129] rvest_1.0.4