gwas分析群体画进化树

我用示例文件报错也是这个。用自己文件也是 ../scripts/ggtree.r -t fasttree.nwk -f ../data/pop_group.txt -g GROUP -n fasttree 这个是我给的命令行

 WARNING: ignoring environment value of R_HOME

--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/

--> R beginners ? I suggest your  learning  R language: https://study.omicsclass.com/index

Registered S3 methods overwritten by 'treeio':

  method              from

  MRCA.phylo          tidytree

  MRCA.treedata       tidytree

  Nnode.treedata      tidytree

  Ntip.treedata       tidytree

  ancestor.phylo      tidytree

  ancestor.treedata   tidytree

  child.phylo         tidytree

  child.treedata      tidytree

  full_join.phylo     tidytree

  full_join.treedata  tidytree

  groupClade.phylo    tidytree

  groupClade.treedata tidytree

  groupOTU.phylo      tidytree

  groupOTU.treedata   tidytree

  is.rooted.treedata  tidytree

  nodeid.phylo        tidytree

  nodeid.treedata     tidytree

  nodelab.phylo       tidytree

  nodelab.treedata    tidytree

  offspring.phylo     tidytree

  offspring.treedata  tidytree

  parent.phylo        tidytree

  parent.treedata     tidytree

  root.treedata       tidytree

  rootnode.phylo      tidytree

  sibling.phylo       tidytree

ggtree v3.6.2 For help: https://yulab-smu.top/treedata-book/


If you use the ggtree package suite in published research, please cite

the appropriate paper(s):


Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk 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. doi:10.1111/2041-210X.12628


Guangchuang Yu. Using ggtree to visualize data on tree-like structures.

Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96


S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L

Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact

visualization of richly annotated phylogenetic data. Molecular Biology

and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166

       Group

Line1 GROUP1

Line2 GROUP1

Line3 GROUP1

Line4 GROUP1

Line5 GROUP1

Line6 GROUP1

Error in `[.data.frame`(groupfile, , opt$group) :

  undefined columns selected

Calls: split -> split.default -> [ -> [.data.frame

Execution halted

请先 登录 后评论

1 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

这个进化树绘制不出来可以使用ITOL或者evolview展示:https://www.omicsclass.com/article/963 

https://www.omicsclass.com/article/417 

请先 登录 后评论
  • 1 关注
  • 0 收藏,94 浏览
  • Wang J 提出于 2024-02-08 10:17

相似问题