Last updated: 2022-01-07

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Knit directory: MS_lesions/

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  • plot_paga_all_wm_gm
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Unstaged changes:
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    Modified:   analysis/ms11_paga.Rmd
    Modified:   analysis/ms13_labelling.Rmd
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    Modified:   code/ms11_paga.R
    Modified:   code/ms11_paga_fns.py
    Modified:   code/ms14_lesions.R
    Modified:   code/supp07_superclean.R
    Modified:   code/supp10_muscat.R

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File Version Author Date Message
Rmd 93fa77e wmacnair 2022-01-05 Add superclean PAGA analysis
html 93fa77e wmacnair 2022-01-05 Add superclean PAGA analysis
Rmd ff2b8fb wmacnair 2021-12-15 Update PAGA analysis, including colouring with ANCOM
html ff2b8fb wmacnair 2021-12-15 Update PAGA analysis, including colouring with ANCOM
html 7fb1b95 wmacnair 2021-11-25 Host with GitLab.
Rmd 58205c2 Macnair 2021-05-21 Update with random effects and markers
Rmd eef8a1c Macnair 2021-04-29 Minor tweaks to allow rerunning on Roche servers
Rmd 129c53d Macnair 2021-04-16 Renamed a lot of things to add ms07_soup

Setup / definitions

Libraries

Helper functions

source('code/ms00_utils.R')
source('code/ms09_ancombc_mixed.R')
source('code/ms11_paga.R')
use_condaenv('scanpy', required=TRUE)
source_python('code/ms11_paga_fns.py')

Inputs

# define inputs
graph_f     = 'output/ms04_conos/conos_graph_2021-02-11.txt'

# define run
labels_f    = 'data/byhand_markers/validation_markers_2021-05-31.csv'
labelled_f  = 'output/ms13_labelling/conos_labelled_2021-05-31.txt.gz'
meta_f      = "data/metadata/metadata_checked_assumptions_2021-10-08.xlsx"

Outputs

save_dir      = 'output/ms11_paga'
if (!dir.exists(save_dir))
  dir.create(save_dir)
date_tag      = '2022-01-07'
seed          = 20220107

# do in parallel
n_cores       = 8

# identifying strange samples
neuro_mad_cut = 2
log_n_mad_cut = 3

# where to save files with subgraphs?
subg_pat      = sprintf('%s/subgraph_%s_%s.txt.gz', save_dir, '%s', date_tag)

# define subsets to run
subset_list = list(
  all         = list(), 
  healthy_WM  = list(lesion_type = c('WM')), 
  MS_WM       = list(lesion_type = c('NAWM', 'AL', 'CAL', 'CIL', 'RL')),
  healthy_GM  = list(lesion_type = c('GM')),
  MS_GM       = list(lesion_type = c('NAGM', 'GML'))
  )
lesion_list = lapply(lesion_ord, function(l) 
  list(lesion_type = l)) %>% 
    setNames(paste0('lesion_', lesion_ord)
  )
xy_ref_list = c(rep('WM', 6), rep('GM', 3)) %>% 
  paste0('healthy_', .) %>% setNames(names(lesion_list))

# what to look at when comparing edges across samples?
sel_broad     = c('Oligodendrocytes', 'OPCs / COPs')
assert_that(all(sel_broad %in% broad_ord))
[1] TRUE
# define ancom outputs to use
ancom_dir     = 'output/ms09_ancombc'
ancom_stamp   = '2021-11-12'
ancom_tags    = c(WM = "lesions_WM", GM = "lesions_GM_4pcs")
ancom_fs      = sapply(ancom_tags, function(t)
  sprintf('%s/ancombc_bootstrap_%s_%s.txt.gz', ancom_dir, t, ancom_stamp)) %>%
  setNames(names(ancom_tags))

Load inputs

meta_dt     = load_meta_dt_from_xls(meta_f)
labels_dt   = load_names_dt(labels_f) %>%
  .[, cluster_id := type_fine]
conos_dt    = load_labelled_dt(labelled_f, labels_f) %>%
  merge(meta_dt, by = 'sample_id') %>%
  add_neuro_props(mad_cut = neuro_mad_cut)
# check for any outliers
size_chks   = calc_size_outliers(conos_dt, mad_cut = log_n_mad_cut)
message("these samples excluded to outlier sample sizes:")
these samples excluded to outlier sample sizes:
print(size_chks[ size_ok == FALSE ])
   matter sample_id   N med_log_N mad_log_N size_ok
1:     GM     EU034 911  8.519391  0.423111   FALSE
2:     GM     EU043 687  8.519391  0.423111   FALSE
# exclude them from conos
ok_samples  = size_chks[ size_ok == TRUE]$sample_id
conos_dt    = conos_dt[ (sample_id %in% ok_samples) & (neuro_ok == TRUE) ]
# make list of all samples
samples     = unique(conos_dt$sample_id)
sample_list = lapply(samples, function(s) list(sample_id = s)) %>% 
  setNames(paste0('sample_', samples))
conos_tidy  = conos_dt[, .(sample_id, matter, lesion_type, cell_id, type_broad, type_fine)]
# fwrite(conos_tidy, file = sprintf('output/ms11_paga/conos_tidy_%s.txt.gz', date_tag)
ancom_ls    = ancom_fs %>% lapply(function(f) fread(f) %>% 
    .calc_boots_sum(min_effect = 0.1, q_cut = 0.05, signif_cut = 0.8)) %>%
  setNames(names(ancom_fs))

Processing / calculations

# make subgraphs for each specification
set.seed(seed)
calc_subgraphs(conos_tidy, subset_list, graph_f, subg_pat, n_sample = 1e5)
already done!
NULL
calc_subgraphs(conos_tidy, lesion_list, graph_f, subg_pat, n_sample = 1e5)
already done!
NULL
# calc_subgraphs(conos_tidy, sample_list, graph_f, subg_pat, n_sample = 0)
# # run on each sample
# if (!check_all_done(sample_list, save_dir, date_tag)) {
#   bpparam   = MulticoreParam(workers = n_cores)
#   bpstop()
#   bpstart()
#   ignore_me = bplapply(seq_along(sample_list), function(i) {
#     spec_n    = names(sample_list)[[i]]
#     subg_f    = sprintf(subg_pat, spec_n)
#     run_paga(save_dir, spec_n, date_tag, r_to_py(as.data.frame(conos_tidy)), 
#       subg_f, group_var = 'type_fine')
#   }, BPPARAM = bpparam)
#   bpstop()
# }

# run on each lesion type
if (!check_all_done(lesion_list, save_dir, date_tag)) {
  n_lesions = length(lesion_list)
  bpparam   = MulticoreParam(workers = min(n_lesions, n_cores))
  bpstop()
  bpstart()
  bplapply(seq_along(lesion_list), function(i) {
    spec_n    = names(lesion_list)[[i]]
    subg_f    = sprintf(subg_pat, spec_n)
    run_paga(save_dir, spec_n, date_tag, r_to_py(as.data.frame(conos_tidy)), 
      subg_f, group_var = 'type_fine')
  }, BPPARAM = bpparam)
  bpstop()
}

# run on each subset
if (!check_all_done(subset_list, save_dir, date_tag)) {
  bpparam   = MulticoreParam(workers = length(subset_list))
  bpstop()
  bpstart()
  bplapply(seq_along(subset_list), function(i) {
    # define things
    spec_n    = names(subset_list)[[i]]
    subg_f    = sprintf(subg_pat, spec_n)

    # run paga
    run_paga(save_dir, spec_n, date_tag, r_to_py(as.data.frame(conos_tidy)), 
      subg_f, group_var = 'type_fine')
  }, BPPARAM = bpparam)
  bpstop()
}
edges_all   = calc_edges_over_samples(sample_list, date_tag, 
  sel_broad, labels_dt)
edges_all   = merge(edges_all, meta_dt, by = 'sample_id')

Analysis

PAGA on all celltypes

Split by GM / WM + condition

for (nn in names(subset_list)) {
  cat('#### ', nn, '\n')
  suppressWarnings({print(plot_paga_outputs(save_dir, nn, date_tag, 'all', 
    conos_dt, subset_list[[nn]], labels_dt, xy_ref = nn))})
  cat('\n\n')
}

all

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healthy_WM

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MS_WM

Version Author Date
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healthy_GM

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MS_GM

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Split by lesion type

for (nn in names(lesion_list)) {
  cat('#### ', nn, '\n')
  suppressWarnings({print(plot_paga_outputs(save_dir, nn, date_tag, 'all', 
    conos_dt, lesion_list[[nn]], labels_dt, xy_ref = nn))})
  cat('\n\n')
}

lesion_WM

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lesion_NAWM

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lesion_AL

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lesion_CAL

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lesion_CIL

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lesion_RL

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lesion_GM

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lesion_NAGM

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lesion_GML

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7fb1b95 wmacnair 2021-11-25

PAGA on oligo + OPC compartment

Split by GM / WM + condition

for (nn in names(subset_list)) {
  cat('#### ', nn, '\n')
  suppressWarnings({print(plot_paga_outputs(save_dir, nn, date_tag, 'olg', 
    conos_dt, subset_list[[nn]], labels_dt, xy_ref = nn))})
  cat('\n\n')
}

all

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healthy_WM

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MS_WM

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healthy_GM

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MS_GM

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Split by lesion type

for (nn in names(lesion_list)) {
  cat('#### ', nn, '\n')
  suppressWarnings({print(plot_paga_outputs(save_dir, nn, date_tag, 'olg', 
    conos_dt, lesion_list[[nn]], labels_dt, xy_ref = nn))})
  cat('\n\n')
}

lesion_WM

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lesion_NAWM

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lesion_AL

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lesion_CAL

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lesion_CIL

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lesion_RL

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lesion_GM

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lesion_NAGM

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lesion_GML

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Split by lesion type, annotated by ANCOM coefficients

for (nn in names(lesion_list)) {
  cat('#### ', nn, '\n')
  ctrl_sample   = xy_ref_list[[nn]] %>% str_match("(lesion|healthy)_(.+)") %>% .[3]
  ancom_dt      = ancom_ls[[ ctrl_sample ]]
  suppressWarnings({print(plot_paga_w_ancom(save_dir, nn, date_tag, 'olg', 
    conos_dt, lesion_list[[nn]], labels_dt, xy_ref = "all",
    ancom_dt, max_fc = 8))})
  cat('\n\n')
}

lesion_WM

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lesion_NAWM

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lesion_AL

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lesion_CAL

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lesion_CIL

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lesion_RL

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lesion_GM

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lesion_NAGM

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lesion_GML

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Heatmap of PAGA edges across samples, within oligo + OPC compartment

cat('### Data-driven')
draw(plot_edge_heatmap(edges_all, conos_dt, split = 'data'))
cat('\n')
cat('### Data-driven, no outliers')
draw(plot_edge_heatmap(edges_all, conos_dt[neuro_ok == TRUE], split = 'data'))
cat('\n')
cat('### Data-driven, WM no outliers')
draw(plot_edge_heatmap(edges_all, conos_dt[neuro_ok == TRUE & matter == 'WM'], 
  split = 'data'))
cat('\n')
cat('### Data-driven, GM no outliers')
draw(plot_edge_heatmap(edges_all, conos_dt[neuro_ok == TRUE & matter == 'GM'], 
  split = 'data'))
cat('\n')
cat('### Split by lesion')
draw(plot_edge_heatmap(edges_all, conos_dt, split = 'lesion_type'))
cat('\n')
cat('### Split by lesion, no outliers')
draw(plot_edge_heatmap(edges_all, conos_dt[neuro_ok == TRUE], split = 'lesion_type'))
cat('\n')

Outputs

devtools::session_info()
- Session info ---------------------------------------------------------------
 setting  value                       
 version  R version 4.0.5 (2021-03-31)
 os       CentOS Linux 7 (Core)       
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    C                           
 tz       Europe/Zurich               
 date     2022-01-07                  

- Packages -------------------------------------------------------------------
 package        * version  date       lib source                            
 ade4             1.7-18   2021-09-16 [1] CRAN (R 4.0.5)                    
 ANCOMBC        * 1.0.5    2021-03-09 [1] Bioconductor                      
 ape              5.5      2021-04-25 [1] CRAN (R 4.0.3)                    
 assertthat     * 0.2.1    2019-03-21 [2] CRAN (R 4.0.0)                    
 beeswarm         0.4.0    2021-06-01 [1] CRAN (R 4.0.3)                    
 Biobase          2.50.0   2020-10-27 [1] Bioconductor                      
 BiocGenerics     0.36.1   2021-04-16 [1] Bioconductor                      
 BiocManager      1.30.16  2021-06-15 [1] CRAN (R 4.0.3)                    
 BiocParallel   * 1.24.1   2020-11-06 [1] Bioconductor                      
 BiocStyle      * 2.18.1   2020-11-24 [1] Bioconductor                      
 biomformat       1.18.0   2020-10-27 [1] Bioconductor                      
 Biostrings       2.58.0   2020-10-27 [1] Bioconductor                      
 bslib            0.3.1    2021-10-06 [2] CRAN (R 4.0.5)                    
 cachem           1.0.6    2021-08-19 [1] CRAN (R 4.0.5)                    
 Cairo            1.5-12.2 2020-07-07 [2] CRAN (R 4.0.2)                    
 callr            3.7.0    2021-04-20 [2] CRAN (R 4.0.3)                    
 cellranger       1.1.0    2016-07-27 [2] CRAN (R 4.0.0)                    
 circlize       * 0.4.13   2021-06-09 [1] CRAN (R 4.0.3)                    
 cli              3.0.1    2021-07-17 [1] CRAN (R 4.0.3)                    
 clue             0.3-60   2021-10-11 [1] CRAN (R 4.0.5)                    
 cluster          2.1.2    2021-04-17 [2] CRAN (R 4.0.3)                    
 codetools        0.2-18   2020-11-04 [2] CRAN (R 4.0.3)                    
 colorout       * 1.2-2    2021-04-15 [1] Github (jalvesaq/colorout@79931fd)
 colorspace       2.0-2    2021-06-24 [1] CRAN (R 4.0.3)                    
 ComplexHeatmap * 2.6.2    2020-11-12 [1] Bioconductor                      
 crayon           1.4.1    2021-02-08 [2] CRAN (R 4.0.3)                    
 data.table     * 1.14.2   2021-09-27 [2] CRAN (R 4.0.5)                    
 DBI              1.1.1    2021-01-15 [2] CRAN (R 4.0.3)                    
 desc             1.4.0    2021-09-28 [1] CRAN (R 4.0.5)                    
 devtools         2.4.2    2021-06-07 [1] CRAN (R 4.0.3)                    
 digest           0.6.28   2021-09-23 [2] CRAN (R 4.0.5)                    
 dplyr            1.0.7    2021-06-18 [2] CRAN (R 4.0.3)                    
 ellipsis         0.3.2    2021-04-29 [2] CRAN (R 4.0.3)                    
 evaluate         0.14     2019-05-28 [2] CRAN (R 4.0.0)                    
 fansi            0.5.0    2021-05-25 [2] CRAN (R 4.0.3)                    
 farver           2.1.0    2021-02-28 [2] CRAN (R 4.0.3)                    
 fastmap          1.1.0    2021-01-25 [2] CRAN (R 4.0.3)                    
 forcats        * 0.5.1    2021-01-27 [2] CRAN (R 4.0.3)                    
 foreach          1.5.1    2020-10-15 [2] CRAN (R 4.0.3)                    
 fs               1.5.0    2020-07-31 [2] CRAN (R 4.0.2)                    
 generics         0.1.1    2021-10-25 [2] CRAN (R 4.0.5)                    
 GetoptLong       1.0.5    2020-12-15 [1] CRAN (R 4.0.3)                    
 ggbeeswarm     * 0.6.0    2017-08-07 [1] CRAN (R 4.0.3)                    
 ggplot2        * 3.3.5    2021-06-25 [1] CRAN (R 4.0.3)                    
 ggrepel        * 0.9.1    2021-01-15 [2] CRAN (R 4.0.3)                    
 git2r            0.28.0   2021-01-10 [1] CRAN (R 4.0.3)                    
 GlobalOptions    0.1.2    2020-06-10 [1] CRAN (R 4.0.3)                    
 glue             1.4.2    2020-08-27 [2] CRAN (R 4.0.3)                    
 gridExtra        2.3      2017-09-09 [2] CRAN (R 4.0.0)                    
 gtable           0.3.0    2019-03-25 [2] CRAN (R 4.0.0)                    
 here             1.0.1    2020-12-13 [2] CRAN (R 4.0.5)                    
 highr            0.9      2021-04-16 [2] CRAN (R 4.0.3)                    
 htmltools        0.5.2    2021-08-25 [2] CRAN (R 4.0.5)                    
 httpuv           1.6.3    2021-09-09 [2] CRAN (R 4.0.5)                    
 ica            * 1.0-2    2018-05-24 [2] CRAN (R 4.0.0)                    
 igraph           1.2.7    2021-10-15 [2] CRAN (R 4.0.5)                    
 IRanges          2.24.1   2020-12-12 [1] Bioconductor                      
 iterators        1.0.13   2020-10-15 [2] CRAN (R 4.0.3)                    
 janitor          2.1.0    2021-01-05 [1] CRAN (R 4.0.3)                    
 jquerylib        0.1.4    2021-04-26 [2] CRAN (R 4.0.3)                    
 jsonlite         1.7.2    2020-12-09 [2] CRAN (R 4.0.3)                    
 knitr            1.36     2021-09-29 [1] CRAN (R 4.0.5)                    
 labeling         0.4.2    2020-10-20 [2] CRAN (R 4.0.3)                    
 later            1.3.0    2021-08-18 [2] CRAN (R 4.0.5)                    
 lattice          0.20-45  2021-09-22 [2] CRAN (R 4.0.5)                    
 lifecycle        1.0.1    2021-09-24 [2] CRAN (R 4.0.5)                    
 lubridate        1.8.0    2021-10-07 [2] CRAN (R 4.0.5)                    
 magrittr       * 2.0.1    2020-11-17 [1] CRAN (R 4.0.3)                    
 MASS           * 7.3-54   2021-05-03 [2] CRAN (R 4.0.3)                    
 Matrix           1.3-4    2021-06-01 [2] CRAN (R 4.0.3)                    
 matrixStats      0.61.0   2021-09-17 [1] CRAN (R 4.0.5)                    
 memoise          2.0.0    2021-01-26 [1] CRAN (R 4.0.3)                    
 mgcv             1.8-38   2021-10-06 [1] CRAN (R 4.0.5)                    
 microbiome       1.12.0   2020-10-27 [1] Bioconductor                      
 multtest         2.46.0   2020-10-27 [1] Bioconductor                      
 munsell          0.5.0    2018-06-12 [2] CRAN (R 4.0.0)                    
 nlme             3.1-153  2021-09-07 [2] CRAN (R 4.0.5)                    
 nloptr           1.2.2.2  2020-07-02 [1] CRAN (R 4.0.3)                    
 patchwork      * 1.1.1    2020-12-17 [2] CRAN (R 4.0.3)                    
 permute          0.9-5    2019-03-12 [1] CRAN (R 4.0.3)                    
 phyloseq       * 1.34.0   2020-10-27 [1] Bioconductor                      
 pillar           1.6.4    2021-10-18 [1] CRAN (R 4.0.5)                    
 pkgbuild         1.2.0    2020-12-15 [1] CRAN (R 4.0.3)                    
 pkgconfig        2.0.3    2019-09-22 [2] CRAN (R 4.0.0)                    
 pkgload          1.2.3    2021-10-13 [2] CRAN (R 4.0.5)                    
 plyr             1.8.6    2020-03-03 [2] CRAN (R 4.0.0)                    
 png              0.1-7    2013-12-03 [2] CRAN (R 4.0.0)                    
 prettyunits      1.1.1    2020-01-24 [2] CRAN (R 4.0.0)                    
 processx         3.5.2    2021-04-30 [2] CRAN (R 4.0.3)                    
 promises         1.2.0.1  2021-02-11 [2] CRAN (R 4.0.3)                    
 ps               1.6.0    2021-02-28 [2] CRAN (R 4.0.3)                    
 purrr          * 0.3.4    2020-04-17 [2] CRAN (R 4.0.0)                    
 R.methodsS3      1.8.1    2020-08-26 [1] CRAN (R 4.0.3)                    
 R.oo             1.24.0   2020-08-26 [1] CRAN (R 4.0.3)                    
 R.utils          2.11.0   2021-09-26 [1] CRAN (R 4.0.5)                    
 R6               2.5.1    2021-08-19 [2] CRAN (R 4.0.5)                    
 rappdirs         0.3.3    2021-01-31 [2] CRAN (R 4.0.3)                    
 rbibutils        2.2.4    2021-10-11 [1] CRAN (R 4.0.5)                    
 RColorBrewer   * 1.1-2    2014-12-07 [2] CRAN (R 4.0.0)                    
 Rcpp             1.0.7    2021-07-07 [1] CRAN (R 4.0.3)                    
 Rdpack           2.1.2    2021-06-01 [1] CRAN (R 4.0.3)                    
 readxl         * 1.3.1    2019-03-13 [2] CRAN (R 4.0.0)                    
 remotes          2.4.1    2021-09-29 [1] CRAN (R 4.0.5)                    
 reshape2         1.4.4    2020-04-09 [2] CRAN (R 4.0.0)                    
 reticulate     * 1.22     2021-09-17 [2] CRAN (R 4.0.5)                    
 rhdf5            2.34.0   2020-10-27 [1] Bioconductor                      
 rhdf5filters     1.2.1    2021-05-03 [1] Bioconductor                      
 Rhdf5lib         1.12.1   2021-01-26 [1] Bioconductor                      
 rjson            0.2.20   2018-06-08 [1] CRAN (R 4.0.3)                    
 rlang            0.4.12   2021-10-18 [2] CRAN (R 4.0.5)                    
 rmarkdown        2.11     2021-09-14 [1] CRAN (R 4.0.5)                    
 rprojroot        2.0.2    2020-11-15 [2] CRAN (R 4.0.3)                    
 Rtsne            0.15     2018-11-10 [2] CRAN (R 4.0.0)                    
 S4Vectors        0.28.1   2020-12-09 [1] Bioconductor                      
 sass             0.4.0    2021-05-12 [2] CRAN (R 4.0.3)                    
 scales         * 1.1.1    2020-05-11 [2] CRAN (R 4.0.0)                    
 sessioninfo      1.1.1    2018-11-05 [1] CRAN (R 4.0.3)                    
 shape            1.4.6    2021-05-19 [1] CRAN (R 4.0.1)                    
 snakecase        0.11.0   2019-05-25 [1] CRAN (R 4.0.3)                    
 stringi          1.7.4    2021-08-25 [1] CRAN (R 4.0.5)                    
 stringr        * 1.4.0    2019-02-10 [2] CRAN (R 4.0.0)                    
 survival         3.2-13   2021-08-24 [2] CRAN (R 4.0.5)                    
 testthat         3.1.0    2021-10-04 [2] CRAN (R 4.0.5)                    
 tibble           3.1.5    2021-09-30 [1] CRAN (R 4.0.5)                    
 tidyr            1.1.4    2021-09-27 [2] CRAN (R 4.0.5)                    
 tidyselect       1.1.1    2021-04-30 [2] CRAN (R 4.0.3)                    
 usethis          2.1.2    2021-10-25 [1] CRAN (R 4.0.5)                    
 utf8             1.2.2    2021-07-24 [1] CRAN (R 4.0.3)                    
 vctrs            0.3.8    2021-04-29 [2] CRAN (R 4.0.3)                    
 vegan            2.5-7    2020-11-28 [1] CRAN (R 4.0.3)                    
 vipor            0.4.5    2017-03-22 [1] CRAN (R 4.0.3)                    
 viridis        * 0.6.2    2021-10-13 [1] CRAN (R 4.0.5)                    
 viridisLite    * 0.4.0    2021-04-13 [1] CRAN (R 4.0.1)                    
 whisker          0.4      2019-08-28 [1] CRAN (R 4.0.3)                    
 withr            2.4.2    2021-04-18 [2] CRAN (R 4.0.3)                    
 workflowr      * 1.6.2    2020-04-30 [1] CRAN (R 4.0.3)                    
 xfun             0.27     2021-10-18 [1] CRAN (R 4.0.5)                    
 XVector          0.30.0   2020-10-27 [1] Bioconductor                      
 yaml             2.2.1    2020-02-01 [2] CRAN (R 4.0.3)                    
 zlibbioc         1.36.0   2020-10-27 [1] Bioconductor                      

[1] /pstore/home/macnairw/lib/conda_r3.12
[2] /pstore/home/macnairw/.conda/envs/r_4.0.3/lib/R/library

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /pstore/home/macnairw/.conda/envs/r_4.0.3/lib/libopenblasp-r0.3.12.so

locale:
 [1] LC_CTYPE=C                 LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BiocParallel_1.24.1  ComplexHeatmap_2.6.2 ggbeeswarm_0.6.0    
 [4] ggrepel_0.9.1        reticulate_1.22      MASS_7.3-54         
 [7] phyloseq_1.34.0      ANCOMBC_1.0.5        ica_1.0-2           
[10] purrr_0.3.4          patchwork_1.1.1      readxl_1.3.1        
[13] forcats_0.5.1        ggplot2_3.3.5        scales_1.1.1        
[16] viridis_0.6.2        viridisLite_0.4.0    assertthat_0.2.1    
[19] stringr_1.4.0        data.table_1.14.2    magrittr_2.0.1      
[22] circlize_0.4.13      RColorBrewer_1.1-2   BiocStyle_2.18.1    
[25] colorout_1.2-2       workflowr_1.6.2     

loaded via a namespace (and not attached):
  [1] plyr_1.8.6          igraph_1.2.7        splines_4.0.5      
  [4] usethis_2.1.2       digest_0.6.28       foreach_1.5.1      
  [7] htmltools_0.5.2     fansi_0.5.0         memoise_2.0.0      
 [10] cluster_2.1.2       remotes_2.4.1       Biostrings_2.58.0  
 [13] matrixStats_0.61.0  R.utils_2.11.0      prettyunits_1.1.1  
 [16] colorspace_2.0-2    rappdirs_0.3.3      rbibutils_2.2.4    
 [19] xfun_0.27           dplyr_1.0.7         callr_3.7.0        
 [22] crayon_1.4.1        jsonlite_1.7.2      survival_3.2-13    
 [25] iterators_1.0.13    ape_5.5             glue_1.4.2         
 [28] gtable_0.3.0        zlibbioc_1.36.0     XVector_0.30.0     
 [31] GetoptLong_1.0.5    pkgbuild_1.2.0      Rhdf5lib_1.12.1    
 [34] shape_1.4.6         BiocGenerics_0.36.1 DBI_1.1.1          
 [37] Rcpp_1.0.7          clue_0.3-60         stats4_4.0.5       
 [40] ellipsis_0.3.2      pkgconfig_2.0.3     R.methodsS3_1.8.1  
 [43] farver_2.1.0        sass_0.4.0          utf8_1.2.2         
 [46] janitor_2.1.0       here_1.0.1          tidyselect_1.1.1   
 [49] labeling_0.4.2      rlang_0.4.12        reshape2_1.4.4     
 [52] later_1.3.0         munsell_0.5.0       cellranger_1.1.0   
 [55] tools_4.0.5         cachem_1.0.6        cli_3.0.1          
 [58] generics_0.1.1      ade4_1.7-18         devtools_2.4.2     
 [61] evaluate_0.14       biomformat_1.18.0   fastmap_1.1.0      
 [64] yaml_2.2.1          processx_3.5.2      knitr_1.36         
 [67] fs_1.5.0            nlme_3.1-153        whisker_0.4        
 [70] R.oo_1.24.0         compiler_4.0.5      beeswarm_0.4.0     
 [73] png_0.1-7           testthat_3.1.0      tibble_3.1.5       
 [76] bslib_0.3.1         stringi_1.7.4       ps_1.6.0           
 [79] highr_0.9           desc_1.4.0          lattice_0.20-45    
 [82] Matrix_1.3-4        nloptr_1.2.2.2      vegan_2.5-7        
 [85] microbiome_1.12.0   permute_0.9-5       multtest_2.46.0    
 [88] vctrs_0.3.8         pillar_1.6.4        lifecycle_1.0.1    
 [91] rhdf5filters_1.2.1  BiocManager_1.30.16 Rdpack_2.1.2       
 [94] jquerylib_0.1.4     GlobalOptions_0.1.2 httpuv_1.6.3       
 [97] R6_2.5.1            promises_1.2.0.1    gridExtra_2.3      
[100] vipor_0.4.5         IRanges_2.24.1      sessioninfo_1.1.1  
[103] codetools_0.2-18    pkgload_1.2.3       rhdf5_2.34.0       
[106] rprojroot_2.0.2     rjson_0.2.20        withr_2.4.2        
[109] S4Vectors_0.28.1    mgcv_1.8-38         parallel_4.0.5     
[112] tidyr_1.1.4         rmarkdown_2.11      snakecase_0.11.0   
[115] Cairo_1.5-12.2      Rtsne_0.15          git2r_0.28.0       
[118] Biobase_2.50.0      lubridate_1.8.0