xiangpin
commented
2 years ago You can use mp_extract_tree with specific tip.level what you want.
> library(MicrobiotaProcess)
MicrobiotaProcess v1.7.8 For help:
https://github.com/YuLab-SMU/MicrobiotaProcess/issues
If you use MicrobiotaProcess in published research, please cite the
paper:
S Xu, L Zhan, W Tang, Z Dai, L Zhou, T Feng, M Chen, S Liu, X Fu, T Wu,
E Hu, G Yu. MicrobiotaProcess: A comprehensive R package for managing
and analyzing microbiome and other ecological data within the tidy
framework. 04 February 2022, PREPRINT (Version 1) available at Research
Square [https://doi.org/10.21203/rs.3.rs-1284357/v1]
This message can be suppressed by:
suppressPackageStartupMessages(library(MicrobiotaProcess))
> data(mouse.time.mpse)
> mouse.time.mpse %>% mp_rrarefy() %>% mp_diff_analysis(.abundance=RareAbundance, .group=time) %>% mp_extract_tree(tip.level=Genus)
The otutree is empty in the MPSE object!
'treedata' S4 object'.
...@ phylo:
Phylogenetic tree with 57 tips and 67 internal nodes.
Tip labels:
g__Bifidobacterium, g__Olsenella, g__Enterorhabdus, g__Bacteroides,
g__un_f__Muribaculaceae, g__Alistipes, ...
Node labels:
r__root, k__Bacteria, p__Actinobacteria, p__Bacteroidetes, p__Cyanobacteria,
p__Deinococcus-Thermus, ...
Rooted; no branch lengths.
with the following features available:
'nodeClass', 'nodeDepth', 'RareAbundanceBySample', 'LDAupper', 'LDAmean',
'LDAlower', 'Sign_time', 'pvalue', 'fdr'.
# The associated data tibble abstraction: 124 × 12
# The 'node', 'label' and 'isTip' are from the phylo tree.
node label isTip nodeClass nodeDepth RareAbundanceByS… LDAupper LDAmean
<int> <chr> <lgl> <chr> <dbl> <list> <dbl> <dbl>
1 1 g__Bifido… TRUE Genus 6 <tibble [19 × 4]> 3.39 3.36
2 2 g__Olsene… TRUE Genus 6 <tibble [19 × 4]> NA NA
3 3 g__Entero… TRUE Genus 6 <tibble [19 × 4]> NA NA
4 4 g__Bacter… TRUE Genus 6 <tibble [19 × 4]> NA NA
5 5 g__un_f__… TRUE Genus 6 <tibble [19 × 4]> 4.96 4.93
6 6 g__Alisti… TRUE Genus 6 <tibble [19 × 4]> 4.09 4.07
7 7 g__un_o__… TRUE Genus 6 <tibble [19 × 4]> NA NA
8 8 g__Deinoc… TRUE Genus 6 <tibble [19 × 4]> NA NA
9 9 g__Lactob… TRUE Genus 6 <tibble [19 × 4]> NA NA
10 10 g__Strept… TRUE Genus 6 <tibble [19 × 4]> NA NA
# … with 114 more rows, and 4 more variables: LDAlower <dbl>, Sign_time <chr>,
# pvalue <dbl>, fdr <dbl>The result of mp_extract_tree is a treedata class, which can be processed and visualized by tidytree, treeio, ggtree and ggtreeExtra.
taekwonleo-yuhao
Dear developer,
I have a question about how to display the Taxonomy information in the tip labels of the taxa tree.
In my case, I convert the phyloseq object into MPSE format and try to identify biomarkers.
But I want to modify my tree tip labels as Genus. But I keep failing. Could you please show me how to modify them?
Thanks! Yuhao