yulab-smu/shinytempsignal

Explore Temporal and Other Phylogenetic Signals

shinyTempSignal: Explore Temporal and Other Phylogenetic Signals

Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.

If you use shinyTempSignal, please cite:

L Zhan, X Luo, W Xie, XA Zhu, Z Xie, J Lin, L Li, W Tang, R Wang, L Deng, Y Liao, B Liu, Y Cai, Q Wang, S Xu, G Yu. shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals. Journal of Genetics and Genomics 2024. doi: 10.1016/j.jgg.2024.02.004

✍️ Authors

YuLab@SMU https://yulab-smu.top

Installation

# to install cran version
install.packages("shinyTempSignal")

# to install github version
if(!require("remotes")) install.packages("remotes")

remotes::install_github("YuLab-SMU/shinyTempSignal")

Usages

library(shinyTempSignal)
run_shinyTempSignal()

shinytempsignal's Issues

Issue with ggplot2 3.4.0

Hi

We recently released ggplot2 3.4.0 and while we didn’t detect issues with cocktailApp during our tests, CRAN has seen issues after release. This mail is to notify you about this and offer help if there are any issues you have trouble fixing

Kind regards
Thomas Lin Pedersen, ggplot2 maintainer

TODO

• 时间信号与root-to-tip距离回归线
• shiny app
• 检测outliers，并可交互选定剔除
• R包
• 时间信号与其它数据回归？
• root-to-tip distance与其它数据回归?

这个想法，本来是基于ggtree和ape等R包，仿照TempEst, https://pubmed.ncbi.nlm.nih.gov/27774300/，写一个shiny app.

这个事情本身是挺简单的，所以计划是让本科生来完成，并希望可以由本科生独立完成一篇小文章。

那么我觉得要完成目标，还需要后面这两个，毕竟单纯仿没意思，还是需要青出于蓝而胜于蓝。而其他数据，对于ggtree全家桶来说，是非常容易处理的，所以后面两个实现起来，也不难。

PS：有问题，可以在github上开issue讨论，这样方便我拉其他学生进来一起讨论和解答。

The `legend.text.align` theme element is not defined in the element hierarchy.

Hi Yu,

I've been trying to use this tool, but I can't get it work on either my M2 Mac Book Pro (Sonoma 14.3.1 (23D60)) or my Windows 10 PC. In both cases I get the following error when I look at the Temporal Signal plot:

The `legend.text.align` theme element is not defined in the element hierarchy.

The first plot with the phylogenetic tree works and the regression of the RTT seems to work. I have tried all the examples in your new shinyTempSignal paper and I get the same error message on all.

I am using R 3.3.3, the latest github version of ggtree and treeio and the last CRAN vesion of all orher packages (including

EDIT: I used the Firefox web browser to open the shiny app.

Below is the sessionInfo() for my Mac:

R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin23.2.0 (64-bit)
Running under: macOS Sonoma 14.3.1

Matrix products: default
BLAS:   /opt/homebrew/Cellar/openblas/0.3.26/lib/libopenblasp-r0.3.26.dylib 
LAPACK: /opt/homebrew/Cellar/r/4.3.3/lib/R/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

time zone: America/Vancouver
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] shiny_1.8.0           shinyTempSignal_0.0.7

loaded via a namespace (and not attached):
  [1] polynom_1.4-1        attempt_0.3.1        remotes_2.4.2.1     
  [4] rlang_1.1.3          magrittr_2.0.3       shinydashboard_0.7.2
  [7] tseries_0.10-55      compiler_4.3.3       mgcv_1.9-1          
 [10] systemfonts_1.0.5    callr_3.7.5          vctrs_0.6.5         
 [13] quantreg_5.97        quadprog_1.5-8       pkgconfig_2.0.3     
 [16] crayon_1.5.2         fastmap_1.1.1        ellipsis_0.3.2      
 [19] fontawesome_0.5.2    labeling_0.4.3       utf8_1.2.4          
 [22] promises_1.2.1       ps_1.7.6             ragg_1.2.7          
 [25] MatrixModels_0.5-3   purrr_1.0.2          cachem_1.0.8        
 [28] aplot_0.2.2          jsonlite_1.8.8       later_1.3.2         
 [31] ggprism_1.0.4        parallel_4.3.3       R6_2.5.1            
 [34] golem_0.4.1          bslib_0.6.1          lmtest_0.9-40       
 [37] jquerylib_0.1.4      Rcpp_1.0.12          zoo_1.8-12          
 [40] httpuv_1.6.14        Matrix_1.6-5         splines_4.3.3       
 [43] nnet_7.3-19          tidyselect_1.2.0     yaml_2.3.8          
 [46] timeDate_4032.109    curl_5.2.1           processx_3.8.3      
 [49] pkgbuild_1.4.3       lattice_0.22-5       tibble_3.2.1        
 [52] quantmod_0.4.26      treeio_1.27.0.002    withr_3.0.0         
 [55] urca_1.3-3           gridGraphics_0.5-1   desc_1.4.3          
 [58] survival_3.5-8       ggpp_0.5.6           xts_0.13.2          
 [61] confintr_1.0.2       pillar_1.9.0         BiocManager_1.30.22 
 [64] ggtree_3.11.1        shinyjs_2.1.0        ggfun_0.1.4         
 [67] generics_0.1.3       TTR_0.24.4           forecast_8.22.0     
 [70] ggplot2_3.5.0        munsell_0.5.0        scales_1.3.0        
 [73] tidytree_0.4.6       xtable_1.8-4         glue_1.7.0          
 [76] lazyeval_0.2.2       tools_4.3.3          ggpmisc_0.5.5       
 [79] SparseM_1.81         fs_1.6.3             grid_4.3.3          
 [82] tidyr_1.3.1          ape_5.7-1            colorspace_2.1-0    
 [85] nlme_3.1-164         patchwork_1.2.0      fracdiff_1.5-3      
 [88] cli_3.6.2            config_0.3.2         textshaping_0.3.7   
 [91] fansi_1.0.6          dplyr_1.1.4          gtable_0.3.4        
 [94] yulab.utils_0.1.4    sass_0.4.8           digest_0.6.34       
 [97] ggplotify_0.1.2      farver_2.1.1         memoise_2.0.1       
[100] htmltools_0.5.7      lifecycle_1.0.4      shinyWidgets_0.8.2  
[103] mime_0.12            MASS_7.3-60.0.1