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Tag: ggtree
A super-pangenome of the North American wild grape species | Genome Biology
Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…
MSA using ggtree msaplot
MSA using ggtree msaplot 0 Hi, I’m trying to do a protein sequence aligment of orthologues of a ~1000 aminoacid (aa) protein, in R. Normal MSA tools display boxes for each aa, which makes the aligment figure too big for my interests. The only MSA tool that I found that…
Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes
Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015). Article PubMed Google Scholar Kanter, D. R. et al. Nitrogen pollution policy beyond the farm. Nat. Food 1, 27–32 (2020). Article ADS Google Scholar Tian, H. et al. A comprehensive quantification of global…
Analysis of geometric morphometrics and molecular phylogeny for Anopheles species in the Republic of Korea
World Health Organization (WHO). WHO malaria report. 2022 www.who.int/publications/i/item/9789240064898 (2022). Savi, M. K. An overview of malaria transmission mechanisms, control, and modeling. Med. Sci. 11, 3 (2023). Google Scholar Bahk, Y. Y. et al. Epidemiological characteristics of re-emerging vivax malaria in the Republic of Korea (1993–2017). Korean J. Parasitol. 56,…
removeBatchEffect with non-linear model fit
removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…
The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution
FAO, ITPS, GSBI, CBD & EC. State of knowledge of soil biodiversity – Status, challenges and potentialities, Report 2020. (FAO). doi.org/10.4060/cb1928en. 2020. Potapov, A. M. et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biol. Rev. 97, 1057–1117 (2022). Article PubMed Google Scholar García-Palacios, P.,…
itol style + color label issue
hi, based on previous post i tried to reproduce some itol style. It’s working but i can’t add color label. library(ape)library(ggtree) …
Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria
Isolation of phyllosphere isolates All bacterial strains were isolated in June 2021 from the flag leaves of four wheat cultivars (Sheriff, Heerup, Rembrandt and Kvium) grown in an experimental field in Høje Taastrup, near Copenhagen, Denmark. Wheat flag leaves were picked, pooled, and either washed or blended prior to dilution…
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
Hi all, I’m trying to create a SPIA data file for all 483 xml files for the KEGG Orthology (KO) Database. I’m working with a non-model organism that is not supported by KEGG as it’s own organism, so I have to use the KEGG Orthology (KO) Database instead of a…
r – ggtree dense tree issues
I am trying to plot a ggtree but am unfamiliar with how to manipulate the tree properly. I have added a picture of how my tree looks currently. I am unable to properly tell any of the branches apart and am unsure what might have caused this or how to…
Adding a Dendrogram to a ggplot2 Heatmap in R
A potent technique that improves the visualisation of hierarchical clustering patterns inside data is to add a dendrogram to a ggplot2 heatmap in R. Dendrograms shed light on the connections and resemblances among data points, assisting in the discovery of distinct clusters or groups. We will examine how to combine…
Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation
Cultivations and harvest Cupriavidus necator strain DSMZ 428 was grown in Ralstonia Minimal Media (RMM) with 100 mM HEPES pH 7.5 under chemostat conditions in a Photon Systems Instruments Multi-Cultivator MC-1000 OD. Each reactor tube was set up to a volume of 55 mL, OD600 0.05 and 3.5 g/L fructose. Once growth ceased,…
The genomic footprint of whaling and isolation in fin whale populations
Samples and sequencing Tissue samples from 50 fin whales (Balaenoptera physalus) were collected using a standard protocol to obtain skin biopsies from free-ranging cetacean species, which use a small stainless-steel biopsy dart deployed from a crossbow or rifle73,74. These samples were collected throughout the Eastern North Pacific (ENP; N = 30, represented…
r – How to delimit the length in axis.line.x theme for ggplot2
I want to delimited the length of the axis.line.x of a ggplot2 theme. I trying to plot a phylogenetic tree, but I will use mtcars as example to generate geom_point plot, but the problem is the same. data(“mtcars”) head(mtcars, 3) mpg cyl disp hp drat wt qsec vs am gear…
Genomic classification and antimicrobial resistance profiling of Streptococcus pneumoniae and Haemophilus influenza isolates associated with paediatric otitis media and upper respiratory infection | BMC Infectious Diseases
Clinical cohort and sampling We enrolled 150 children into the study with AOM or without AOM but presenting with an URI (see Fig. 1 for a flow chart), obtaining nasopharyngeal (NP) swabs from all enrolled, and 37 additional middle ear fluid (MEF) samples from some of the children with AOM. A…
r – Scale on the y-axis in a tree rotated with ‘layout_dendrogram()’ using ggtree
I’m editing a time-scaled tree using ggtree. The dates are correctly adjusted when I apply the ‘mrsd’ command and ‘theme_tree2()’, but when I try to rotate the tree with ‘layout_dendrogram()’, the scale still remains on the x-axis with no dates. Is there a way to place the date scale on…
Comparative analysis of carbapenem-resistant K. pneumoniae
Introduction The worldwide spread of Klebsiella pneumoniae is a major global public health threat.1,2 K. pneumoniae is an opportunistic pathogen that colonizes the human gut and respiratory tract and possibly causes infection in immunocompromised hosts. Gut colonized K. pneumoniae is one of the important pathogens causing nosocomial infections, although the…
How to get image of mutliple alignment sequence that is labeled by row?
I have been looking at many, many different multiple sequence alignment software packages. There’s a post that I was using earlier from BioStars, but I can’t find it anymore. ADOMA doesn’t produce anything. There is no error message, just blank HTML ESPript, which requires faxing or snail-mailing a license request,…
Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer
Espedido, B. A., Partridge, S. R. & Iredell, J. R. bla(IMP-4) in different genetic contexts in Enterobacteriaceae isolates from Australia. Antimicrob. Agents Chemother. 52, 2984–2987 (2008). Article CAS PubMed PubMed Central Google Scholar Kizny Gordon, A. et al. Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated…
r – Color node points in ggtree: Must request at least one colour from a hue palette
I would like to color the nodes in a tree according to a categorical variable with the help of ggtree. However, I am receiving the error “Must request at least one colour from a hue palette.” I have constructed an example with the example tree from a similar question you…
GGtree flips my tree
GGtree flips my tree 0 Hi, I am generating a tree figure wiith ggtree. But the output keeps coming upside down no matter which parameter I use or change. Does anyone have any idea about this? This is my command line: ggtree_obj <- ggtree(species_tree, ladderize = FALSE, layout = “rectangular”)+…
A genome catalogue of lake bacterial diversity and its drivers at continental scale
Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011). Article CAS PubMed PubMed Central Google Scholar Pernthaler, J. Competition and niche separation of pelagic bacteria in freshwater habitats….
ggplot dot plot by group
If you don’t like that add scales=”free_y”: Thanks for contributing an answer to Stack Overflow! # y axis isn’t really meaningful, so hide it, # Examples with stacking along y axis instead of x, # binpositions=”all” ensures that the bins are aligned between groups, # Stacking multiple groups, with different…
Measuring Evolutionary Distance Between Species from Chronogram
If I’ve interpreted correctly, you want the time to the most recent common ancestor of any two species in the tree? If so, something like the following works: library(“ggtree”) library(“treeio”) require(“dplyr”) beast_file <- system.file(“examples/MCC_FluA_H3.tree”, package=”ggtree”) beast_tree <- read.beast(beast_file) beast_tree@data %>% dplyr::select(node,height) # choose some random tips for the purpose of…
Linking data with phylogenetic tree using ggtree
Linking data with phylogenetic tree using ggtree 0 Hi, I am really new to R and I’m trying to use ggtree module. I have a species tree and some data. I need to link this data with the species in the tree. My dataframe has the tip label names in…
Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history
Dark, P. & Gent, H. Pests and diseases of prehistoric crops: a yield ‘honeymoon’ for early grain crops in Europe? Oxford J. Archaeol. 20, 59–78 (2001). Article Google Scholar Mira, A., Pushker, R. & Rodriguez-Valera, F. The Neolithic revolution of bacterial genomes. Trends Microbiol. 14, 200–206 (2006). Article CAS PubMed …
CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter
Collins FS, Green ED, Guttmacher AE, Guyer MS. US National Human Genome Research Institute. A vision for the future of genomics research. Nature. 2003;422(6934):835–47. Article CAS PubMed Google Scholar Slatko BE, Gardner AF, Ausubel FM. Overview of next-generation sequencing technologies. Curr Protoc Mol Biol. 2018;122(1):e59. Article PubMed PubMed Central Google…
ggtree functions suddenly stopped working: “Error in offspring.tbl_tree_item(…”
I am fairly new to ggtree and it had been working until today. Today, several functions stopped working: — MRCA(), geom_hilight(), and geom_cladelab() I have searched the web for answers. Example: > sessionInfo( ) R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.4.1 Matrix products: default BLAS:…
r – geom_tippoint: How to incorporate the palette I want for the color parameter in ggtree’s geom_tippoint for the tippoints?
I have 2 trees with unequal number of nodes and I want put them together with their tippoints colored according to their taxa. But I am unable to have the same color palette for both the trees, I essentially am looking for a shared legend for the two trees. I…
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages )
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages ) 0 Hello everyone! Yesterday, I tried to install ggtree, enrichplot, and ggtree in my RStudio (verision 4.1.0) but it turned out they couldn’t be successfully installed and a few warning messages popped out, though I had already installed all…
BTN3A3 evasion promotes the zoonotic potential of influenza A viruses
Lipsitch, M. et al. Viral factors in influenza pandemic risk assessment. eLife doi.org/10.7554/eLife.18491 (2016). Afrache, H., Gouret, P., Ainouche, S., Pontarotti, P. & Olive, D. The butyrophilin (BTN) gene family: from milk fat to the regulation of the immune response. Immunogenetics 64, 781–794 (2012). Article CAS PubMed Google Scholar Ye,…
Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential
Sample collection Sampling kits were sent out to various bat rehabilitators in the UK, as described previously56, for the collection of faeces from bats. These faecal samples (0.02–1 g) were immediately stored in 5 ml of RNAlater solution to prevent degradation of RNA. The geographical locations and collection dates for all samples…
Insight into pathogenomics and phylogeography of hypervirulent and highly-lethal Mycobacterium tuberculosis strain cluster | BMC Infectious Diseases
Luo T, Comas I, Luo D, et al. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proc Natl Acad Sci USA. 2015;112:8136–41. Article CAS PubMed PubMed Central Google Scholar Yin QQ, Liu HC, Jiao WW, et al. Evolutionary history and ongoing transmission of phylogenetic…
Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria) | Parasites & Vectors
Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, et al. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018;16:410–22. doi.org/10.1038/s41579-018-0029-9. Article CAS PubMed Google Scholar Blaxter M. Counting angels with DNA. Nature. 2003;421:122–3. doi.org/10.1038/421122a. Article CAS PubMed Google Scholar Cordier T, Alonso-Sáez L, Apothéloz-Perret-Gentil L, Aylagas…
Highly drug resistant clone of Salmonella Kentucky ST198 in clinical infections and poultry in Zimbabwe
Anonymous. Tackling drug resistant infections globally: final report and recommendations. Review on Antimicrobial Resistance. amr-review.org/sites/default/files/160518_Final%20paper_with%20cover.pdf (2016). Antimicrobial Resistance C. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022). Article Google Scholar Klein, E. Y. et al. Global increase and geographic convergence in antibiotic consumption…
A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia
Grimont PAD, W. F. X. Antigenic formulae of the Salmonella serovars, 9th ed. (World health organization collaborating center for reference and research on Salmonella, Insitut Pasteur, 2007). Gal-Mor, O., Boyle, E. C. & Grassl, G. A. Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ….
Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization
Wang, Wei-Lin et al. Application of metagenomics in the human gut microbiome. World J. Gastroenterol. 21, 803–814 (2015). Article ADS PubMed PubMed Central Google Scholar Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2021). Article CAS PubMed Google…
Handling NA’s in Deseq2
Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…
Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range
Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, et al. The population biology of invasive species. Annu Rev Ecol Syst. 2001;32:305–32. Article Google Scholar Allendorf FW, Lundquist LL. Introduction: population biology, evolution, and control of invasive species. Conserv Biol. 2003;17:24–30. Article Google Scholar Erickson AB. The…
lfcshrink error DESeq2
Hello! I’m having problems with lfcShrink in my DESeq2 workflow. I’m trying to do a differential expression analysis (with only one comparison term: “MULTIseq_ID_call2”) on my single-cell data. However when I do lfcShrink I get an error that I cannot interpret. Can you help me? dds <- DESeq(dds, test =…
Long-Read Metagenomics and CAZyme Discovery
La Rosa SL, Ostrowski MP, Vera-Ponce de León A, McKee LS, Larsbrink J, Eijsink VG, Lowe EC, Martens EC, Pope PB (2022) Glycan processing in gut microbiomes. Curr Opin Microbiol 67:102143. doi.org/10.1016/j.mib.2022.102143 CrossRef CAS PubMed Google Scholar Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette…
Whole genome sequencing of Ethiopian Brucella abortus isolates expands the known diversity of an early branching sub-Saharan African lineage
1. Introduction Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella, which affects domestic livestock and a wide range of wild mammals (Ducrotoy et al., 2017). The disease is amongst the most common zoonotic infections globally, with an estimated 500,000 human cases annually (Pappas et al., 2006),…
Is there a software that can compare phylogenetic trees to each othe (face to face comparison)?
Here is a solution with ggtree for face to face trees: library(ggplot2) library(ggtree) library(cowplot) set.seed(8455) t1 <- rtree(20) t2 <- rtree(20) T1 <- ggtree(t1 ) + theme_tree2(legend.position=’none’, plot.margin = unit(c(0,0,0,0),”cm”)) + geom_tiplab() T2 <- ggtree(t2) + theme_tree2(legend.position=’none’, plot.margin = unit(c(0,0,0,0),”cm”)) + geom_tiplab(hjust =1) + scale_x_reverse() d1 = T1$data[T1$data$isTip,] d1$x[] =…
Sensory specializations drive octopus and squid behaviour
van Giesen, L., Kilian, P. B., Allard, C. A. H. & Bellono, N. W. Molecular basis of chemotactile sensation in octopus. Cell 183, 594–604.e14 (2020). Article PubMed PubMed Central Google Scholar Noviello, C. M. et al. Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Cell 184, 2121–2134 (2021)….
Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno
Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article CAS PubMed PubMed Central Google Scholar Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…
Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism
Weight loss and clinical improvements after IF intervention We performed a three-week intervention study on 72 adult Chinese volunteers subjected to a 5:2 program as detailed in Fig. 1a. The volunteers comprised individuals ranging from regular to obese (Supplementary Table 1). Seventeen clinical parameters were determined both before and after…
Annotated dendogram (tree) from tbl_graph
Annotated dendogram (tree) from tbl_graph 0 @ee934b4b Last seen 15 hours ago France Hello, I have a problem because I have little experience with the tbl_graph format and how to use it well with ggtree (or other script to draw a tree). I have created a tbl_graph (from clustree) of…
Latest version of ggtree (3.6.2) unavailable on Anaconda. Only 3.6.0 exists.
Latest version of ggtree (3.6.2) unavailable on Anaconda. Only 3.6.0 exists. 1 @facdaea0 Last seen 11 hours ago Canada Hi there, The latest release 3.6.2 for ggtree is unavailable on the Bioconductor-ggtree Anaconda repository which is creating some dependency issues in conda pulls. Are there obstacles preventing the latest version…
Bioconductor – ggtree
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see ggtree. an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data Bioconductor version: 3.3 ggtree extends the ggplot2 plotting system which implemented the grammar of graphics….
Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota
Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007). Article CAS PubMed PubMed Central Google Scholar Glöckner, J. et al. Phylogenetic diversity and metagenomics of candidate division OP3. Environ. Microbiol. 12, 1218–1229…
Detection of Streptococcus pyogenes M1UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA
Walker, M. J. et al. Disease manifestations and pathogenic mechanisms of Group A Streptococcus. Clin. Microbiol. Rev. 27, 264–301 (2014). Article PubMed PubMed Central Google Scholar Carapetis, J. R., Steer, A. C., Mulholland, E. K. & Weber, M. The global burden of group A streptococcal diseases. Lancet Infect. Dis. 5,…
Strange Cook’s Values with DESeq2
Hi, I’m currently trying to assess fold change when comparing two different sample types using DESeq2 package and I’m getting weird Cook’s distance values which are causing major problems. The two different samples have different amounts of replicates (6 replicates vs 5 replicates) which might be the reason for these…
Error in UseMethod(“rescale”)
Error in UseMethod(“rescale”) 0 @2528ae94 Last seen 17 hours ago United States While using cnetplot to plot enrichGo results, I am getting the following error. It used to work before, but now I am constantly getting this error. I am using clusterprofiler package gse <- enrichGO(gene = deGenes, ont =…
The genus Serratia revisited by genomics
Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….
bioinformatics – How to attach numbers next to nodes and tips in a tree illustration produced by ggtree? The numbers are imported from an external tsv file
This is a bioinformatic question. For those of you familiar with ggtree, how do I go about annotating numerical information per node and tip in ggtree? Say for example I have a phylogenetic tree, and for each node and tip I have a gene-count. How can I annotate this relevant…
r – ggtree setting height scale
I’m doing microssatellite analysis to understand genetic relationship between fungal isolates. For that I first calculated the Jaccard’s coefficient and then want to generate a dendrogram using UPGMA cluster analysis. I did the following: jacc_coef <- vegdist(HC_df, method = “jaccard”) *100 (HC_df is my data frame) afu_clin.hc <- hclust(d =…
R: ggtree gradient highlight issue
I try to fill two clades with gradient color: set.seed(123) tree <- rtree(31) df <- data.frame(node=c(47, 36), type=c(“A”, “B”)) ggtree(tree) + geom_text2(aes(subset=!isTip, label=node), hjust=-.3) + geom_hilight(data = df, aes(node = node, fill = type), type = “gradient”, graident.direction = ‘rt’, alpha=.6) and get an error instead: Error in fix.by(by.x, x)…
Description, Programming Languages, Similar Projects of Ggtree
🎄Visualization and annotation of phylogenetic trees 206 Projects Similar to Ggtree Tidytuesday 📊 My contributions to the #TidyTuesday challenge Tracklytics ✔️ Annotation based tracking handler with aspect oriented programming Mirador An open-source, web-based ‘multi-up’ viewer that supports zoom-pan-rotate functionality, ability to display/compare simple images, and images with annotations. S Mall…
Questions tagged ggtree – DevDreamz
Python Javascript Linux FAQ LoginSignup PUBLIC All Questions Tags Snippets Jobs ggplot2rdplyrgeom-textggtree ggtreeggtextggplot2r ggplot2rdata-visualizationggtreeggridges PreviousNext Recent Posts show same id one time but in column count how many times php Assign bundle or argument to ImageView in Android ValueRequiredException during RSS feed parsing in Retrofit Yii2 redirecting isn’t working. Why?…
r – Displaying BIC and AICs from MSA nucleotide multisequence fasta file
I am trying to replicate MEGA (models/find best DNA protein models) using R. After reading R AICs and BIC documentation I can’t understand how I can implement it. How can I implement AICs and BICs without having to especify the number of sequences in the fasta file (in case that…
Re: [R] ggtree node labels
Hi If you asked google ggtree node label you will get many hits which tell you how to label nodes E.g. bioc.ism.ac.jp/packages/3.3/bioc/vignettes/ggtree/inst/doc/treeAnnot ation.html And you will get it much more quickly than by asking here. Cheers Petr > —–Original Message—– > From: R-help <r-help-boun…@r-project.org> On Behalf Of April Ettington >…
Plot igraph tree objects with ggtree
This is a good idea. ggtree is designed for phylogenetic analysis. Some of the functionalities may not be applied to other objects like igraph directly. To make the support more smoothly is to convert the igraph object as a phylo object. So that after conversion, ggtree can be used to…
R ggtree: How to label single tree tip with ggtree similar to labeling nodes with geom_cladelabel
I’m having trouble with labeling single tips in my tree with ggtree. I’m trying to highlight and label nodes from a tree with geom_hilight and geom_cladelabel. This seems to work fine with nodes that have more than 1 tree tip, but when I try to label a single tip, I…
hjust in geom_cladelab not working properly
hjust in geom_cladelab not working properly 0 I have an issue with hjust of clade lab when using geom_cladelab. The justification does not change when specifying the labels to align with the outer circle and having angle = “auto” . I have added an reprex of the issue. The problem…