Tag: ggtree
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…
