Problem in changing branch length of outgroup

[Wannarat Yim-im]

Dear all,

       I have tried to follow the code provided in "change branch length of outgroup" explained in FAQ but it did not work with my data.

I have one long branch outgroup and try to make the branch shorter and the line type different from others.

This is the code tried on my data.

x <- read.iqtree("tree4_output_T1_completegenome_outgrouptop.tree")

p <- ggtree(x)

p$data[p$data$node %in% c("VR23-outgroup", "0.8")] <- mean(p$data$x)

The error messages I got

Error: Must assign to columns with a valid subscript vector.

ℹ Logical subscripts must match the size of the indexed input.

x The input has size 11 but the subscript `p$data$node %in% c("VR23-outgroup", "0.8")` has size 232.

I appreciate all suggestions.

Wannarat

[Yu, Guangchuang]

check your code, http://yulab-smu.top/treedata-book/faq.html#change-branch-length-of-outgroup

On Fri, May 8, 2020 at 7:36 AM Wannarat Yim-im <wyi...@iastate.edu> wrote:

Dear all,

       I have tried to follow the code provided in "change branch length of outgroup" explained in FAQ but it did not work with my data.

I have one long branch outgroup and try to make the branch shorter and the line type different from others.

This is the code tried on my data.

x <- read.iqtree("tree4_output_T1_completegenome_outgrouptop.tree")

p <- ggtree(x)

p$data[p$data$node %in% c("VR23-outgroup", "0.8")] <- mean(p$data$x)

Apparently, it should be p$data[p$data$node %in% c("VR23-outgroup", "0.8"), 'x'] <- mean(p$data$x)

The error messages I got

Error: Must assign to columns with a valid subscript vector.

ℹ Logical subscripts must match the size of the indexed input.

x The input has size 11 but the subscript `p$data$node %in% c("VR23-outgroup", "0.8")` has size 232.

I appreciate all suggestions.

Wannarat

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1. G Yu*. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. https://doi.org/10.1002/cpbi.96
2. LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. http://dx.doi.org/10.1093/molbev/msz240
3. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. https://doi.org/10.1093/molbev/msy194
4. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. https://doi.org/10.1111/2041-210X.12628
5. Book: https://yulab-smu.github.io/treedata-book/
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Guangchuang Yu PhD

Professor, Associate Director

Department of Bioinformatics

School of Basic Medical Sciences

Southern Medical University

Guangzhou, China

www: https://guangchuangyu.github.io

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