mp_plot_abundance()功能X轴样本排序

liuninghua521 commented 2 years ago

老师好，新版的物种组成可视化函数中，没有了旧版的sampleLevels参数，该如何设置X轴的样本顺序呢？我没有找到可以为它设置因子顺序的方法，麻烦老师解疑一下，谢谢老师。

xiangpin commented 2 years ago

The .group argument controlled the facet order of the group can be adjusted with dplyr::mutate see also #50. But the order of Sample (actually the colnames of mpse) can not be adjusted, but you can adjust it after the ggplot object is assigned to a variable. see the following.

> library(MicrobiotaProcess)
MicrobiotaProcess v1.9.1 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
# A MPSE-tibble (MPSE object) abstraction: 4,142 × 11
# OTU=218 | Samples=19 | Assays=Abundance | Taxonomy=Kingdom, Phylum, Class, Order, Family, Genus, Species
   OTU    Sample Abundance time  Kingdom Phylum Class Order Family Genus Species
   <chr>  <chr>      <int> <chr> <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>
 1 OTU_1  F3D0         579 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u… s__un_…
 2 OTU_2  F3D0         345 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u… s__un_…
 3 OTU_3  F3D0         449 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u… s__un_…
 4 OTU_4  F3D0         430 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u… s__un_…
 5 OTU_5  F3D0         154 Early k__Bac… p__Ba… c__B… o__B… f__Ba… g__B… s__un_…
 6 OTU_6  F3D0         470 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u… s__un_…
 7 OTU_7  F3D0         282 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u… s__un_…
 8 OTU_8  F3D0         184 Early k__Bac… p__Ba… c__B… o__B… f__Ri… g__A… s__un_…
 9 OTU_9  F3D0          45 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u… s__un_…
10 OTU_10 F3D0         158 Early k__Bac… p__Ba… c__B… o__B… f__Mu… g__u… s__un_…
# … with 4,132 more rows
> mouse.time.mpse %>% colnames()
 [1] "F3D0"   "F3D1"   "F3D141" "F3D142" "F3D143" "F3D144" "F3D145" "F3D146"
 [9] "F3D147" "F3D148" "F3D149" "F3D150" "F3D2"   "F3D3"   "F3D5"   "F3D6"
[17] "F3D7"   "F3D8"   "F3D9"
> mouse.time.mpse %>% mp_rrarefy() %>% mp_plot_abundance(.abundance=RareAbundance,  taxa.class=Phylum) -> p
> p

xx1

Next, you can adjust the order by refactoring the levels of Sample column in p$data.

> mouse.time.mpse %>% colnames() %>% sample() -> yy
> p$data %<>% dplyr::mutate(Sample=factor(Sample, levels=yy))
> p

liuninghua521 commented 2 years ago

谢谢老师解答！

YuLab-SMU / MicrobiotaProcess

mp_plot_abundance()功能X轴样本排序 #61