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YuLab-SMU
:christmas_tree:Visualization and annotation of phylogenetic trees
### Prerequisites Hi, I created a phylogenetic tree from whole genome ANI values 0f 300 strains. When I visualized the tree using ggtree, it had polytomy branches while it was...
Hello, I have been trying to follow the example for aligning genomic features with a phylogenetic tree found here: https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/ This example entails using the ggbio package to visualise genomic...
### Prerequisites + [] Have you read [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x] make sure your are using the latest release version * [x] read the [documents](https://yulab-smu.github.io/treedata-book/) * [x]...
Hi Dr. Yu, When I re-run the "10.1.1 facet_widths" [https://yulab-smu.github.io/treedata-book/chapter10.html#facet-utilities](url) command line is "facet_widths(p2, widths = c(1, 2))"', which leads to the error. I tried to search the solution with...
I have a MSA file and wanted to create tree from it. I created the distance matrix first then created a ggtree for that. Now it works. My issue is...
Dear Prof Yu, I see a wonderful example of the ggtree data in the 7.5 sector. https://yulab-smu.github.io/treedata-book/chapter7.html#gheatmap-ggnewscale library(ggplot2) library(ggtree) set.seed(2019-10-31) tr
Hi, I've been trying to plot a bar chart with community composition together with a hierarchical clustering dendrogram, and while I was able to plot it, there are always some...
I am trying to add an additional layer to tree ``` tree=rtree(10) ggtree(tree, layout="circular") ``` I need my additional layer to contain 10 points aligned horizontally ( ina straight line)...
Hi, I would like to plot a subclade of a large phylogenetic tree using ggtree. The `viewClade()` function is supposed to do the job, but it gives unexpected results when...
The documentation for `geom_treescale` doesn't cover how it is positioned. That is a problem because default values can lead to overplotting of the scale on the tree. ``` library(ape) set.seed(42)...
