Stat: Sample clustering using different linkage method(phyloseq_clustering.py v5.1.0)

## Import packages
library(phyloseq)
library(scales)
library(ape)
source(file.path(params$libdir, "graphical_methods.R"))
## Alternative to source all extra function from a github repo
## source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R")

## Setting variables
  ## The Phyloseq object (format rdata)
  # phyloseq <- ""

  ## The beta diversity distance matrix file
  # distance <- ""

  ## The experiment variable that you want to analyse
  # varExp <- ""

## Create input and parameters dataframe
  # params <- data.frame( "phyloseq" = phylose, "distance" = distance, "varExp" = varExp)

## Load data
  ## the phyloseq object
load(params$phyloseq)

  ## the distance matrix file
A        <- read.table(file=params$distance, row.names=1)
dist     <- as.dist(A)

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Reproducibility token

sessioninfo::session_info()

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       Ubuntu 24.04.2 LTS
 system   x86_64, linux-gnu
 ui       X11
 language fr_FR:en
 collate  en_US.utf8
 ctype    en_US.utf8
 tz       Europe/Paris
 date     2026-01-14
 pandoc   2.19.2 @ /home/maria/miniforge3/envs/frogs@5.1.0/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package          * version   date (UTC) lib source
 ade4               1.7-22    2023-02-06 [1] CRAN (R 4.1.3)
 ape              * 5.7-1     2023-03-13 [1] CRAN (R 4.1.3)
 Biobase            2.54.0    2021-10-26 [1] Bioconductor
 BiocGenerics       0.40.0    2021-10-26 [1] Bioconductor
 biomformat         1.22.0    2021-10-26 [1] Bioconductor
 Biostrings         2.62.0    2021-10-26 [1] Bioconductor
 bitops             1.0-7     2021-04-24 [1] CRAN (R 4.1.3)
 bslib              0.5.0     2023-06-09 [1] CRAN (R 4.1.3)
 cachem             1.0.8     2023-05-01 [1] CRAN (R 4.1.3)
 cli                3.6.1     2023-03-23 [1] CRAN (R 4.1.3)
 cluster            2.1.4     2022-08-22 [1] CRAN (R 4.1.3)
 codetools          0.2-19    2023-02-01 [1] CRAN (R 4.1.3)
 colorspace         2.1-0     2023-01-23 [1] CRAN (R 4.1.3)
 crayon             1.5.2     2022-09-29 [1] CRAN (R 4.1.3)
 data.table         1.14.8    2023-02-17 [1] CRAN (R 4.1.3)
 digest             0.6.31    2022-12-11 [1] CRAN (R 4.1.3)
 dplyr              1.1.2     2023-04-20 [1] CRAN (R 4.1.3)
 evaluate           0.21      2023-05-05 [1] CRAN (R 4.1.3)
 fansi              1.0.4     2023-01-22 [1] CRAN (R 4.1.3)
 farver             2.1.1     2022-07-06 [1] CRAN (R 4.1.3)
 fastmap            1.1.1     2023-02-24 [1] CRAN (R 4.1.3)
 foreach            1.5.2     2022-02-02 [1] CRAN (R 4.1.3)
 generics           0.1.3     2022-07-05 [1] CRAN (R 4.1.3)
 GenomeInfoDb       1.30.1    2022-01-30 [1] Bioconductor
 GenomeInfoDbData   1.2.7     2026-01-14 [1] Bioconductor
 ggplot2          * 3.4.2     2023-04-03 [1] CRAN (R 4.1.3)
 glue               1.6.2     2022-02-24 [1] CRAN (R 4.1.3)
 gtable             0.3.3     2023-03-21 [1] CRAN (R 4.1.3)
 highr              0.10      2022-12-22 [1] CRAN (R 4.1.3)
 htmltools          0.5.5     2023-03-23 [1] CRAN (R 4.1.3)
 igraph             1.3.5     2022-09-22 [1] CRAN (R 4.1.3)
 IRanges            2.28.0    2021-10-26 [1] Bioconductor
 iterators          1.0.14    2022-02-05 [1] CRAN (R 4.1.3)
 jquerylib          0.1.4     2021-04-26 [1] CRAN (R 4.1.3)
 jsonlite           1.8.5     2023-06-05 [1] CRAN (R 4.1.3)
 knitr              1.43      2023-05-25 [1] CRAN (R 4.1.3)
 lattice            0.21-8    2023-04-05 [1] CRAN (R 4.1.3)
 lifecycle          1.0.3     2022-10-07 [1] CRAN (R 4.1.3)
 magrittr           2.0.3     2022-03-30 [1] CRAN (R 4.1.3)
 MASS               7.3-58.3  2023-03-07 [1] CRAN (R 4.1.3)
 Matrix             1.5-4.1   2023-05-18 [1] CRAN (R 4.1.3)
 mgcv               1.8-42    2023-03-02 [1] CRAN (R 4.1.3)
 multtest           2.50.0    2021-10-26 [1] Bioconductor
 munsell            0.5.0     2018-06-12 [1] CRAN (R 4.1.3)
 nlme               3.1-162   2023-01-31 [1] CRAN (R 4.1.3)
 permute            0.9-7     2022-01-27 [1] CRAN (R 4.1.3)
 phyloseq         * 1.38.0    2021-10-26 [1] Bioconductor
 pillar             1.9.0     2023-03-22 [1] CRAN (R 4.1.3)
 pkgconfig          2.0.3     2019-09-22 [1] CRAN (R 4.1.3)
 plyr               1.8.8     2022-11-11 [1] CRAN (R 4.1.3)
 R6                 2.5.1     2021-08-19 [1] CRAN (R 4.1.3)
 Rcpp               1.0.10    2023-01-22 [1] CRAN (R 4.1.3)
 RCurl              1.98-1.12 2023-03-27 [1] CRAN (R 4.1.3)
 reshape2         * 1.4.4     2020-04-09 [1] CRAN (R 4.1.3)
 rhdf5              2.38.1    2022-03-10 [1] Bioconductor
 rhdf5filters       1.6.0     2021-10-26 [1] Bioconductor
 Rhdf5lib           1.16.0    2021-10-26 [1] Bioconductor
 rlang              1.1.1     2023-04-28 [1] CRAN (R 4.1.3)
 rmarkdown          2.22      2023-06-01 [1] CRAN (R 4.1.3)
 rstudioapi         0.14      2022-08-22 [1] CRAN (R 4.1.3)
 S4Vectors          0.32.4    2022-03-24 [1] Bioconductor
 sass               0.4.6     2023-05-03 [1] CRAN (R 4.1.3)
 scales           * 1.2.1     2022-08-20 [1] CRAN (R 4.1.3)
 sessioninfo        1.2.2     2021-12-06 [1] CRAN (R 4.1.3)
 stringi            1.7.6     2021-11-29 [1] CRAN (R 4.1.1)
 stringr            1.5.0     2022-12-02 [1] CRAN (R 4.1.3)
 survival           3.5-5     2023-03-12 [1] CRAN (R 4.1.3)
 tibble             3.2.1     2023-03-20 [1] CRAN (R 4.1.3)
 tidyselect         1.2.0     2022-10-10 [1] CRAN (R 4.1.3)
 utf8               1.2.3     2023-01-31 [1] CRAN (R 4.1.3)
 vctrs              0.6.2     2023-04-19 [1] CRAN (R 4.1.3)
 vegan              2.6-4     2022-10-11 [1] CRAN (R 4.1.3)
 withr              2.5.0     2022-03-03 [1] CRAN (R 4.1.3)
 xfun               0.39      2023-04-20 [1] CRAN (R 4.1.3)
 XVector            0.34.0    2021-10-26 [1] Bioconductor
 yaml               2.3.7     2023-01-23 [1] CRAN (R 4.1.3)
 zlibbioc           1.40.0    2021-10-26 [1] Bioconductor

 [1] /home/maria/miniforge3/envs/frogs@5.1.0/lib/R/library

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