HMP_2012_WMS_gingiva - Supragingival vs subgingival plaque
Source:vignettes/articles/HMP_2012_WMS_gingival.Rmd
HMP_2012_WMS_gingival.Rmd
library(MicrobiomeBenchmarkDataAnalyses)
library(MicrobiomeBenchmarkData)
library(mia)
library(phyloseq)
library(benchdamic)
library(dplyr)
library(purrr)
library(ggplot2)
library(gridExtra)Import data
dat_name <-'HMP_2012_WMS_gingival'
conditions_col <- 'body_subsite'
conditions <- c(condB = 'subgingival_plaque', condA = 'supragingival_plaque')
tse <- getBenchmarkData(dat_name, dryrun = FALSE)[[1]]
tse <- filterTaxa(tse)
colData(tse)[[conditions_col]] <-
factor(colData(tse)[[conditions_col]], levels = conditions)
tse## class: TreeSummarizedExperiment
## dim: 189 16
## metadata(0):
## assays(1): counts
## rownames(189): Streptococcus_parasanguinis Veillonella_dispar ...
## Prevotella_baroniae Propionibacterium_acidifaciens
## rowData names(8): kingdom phylum ... species taxon_annotation
## colnames(16): SRS013949 SRS013950 ... SRS063215 SRS065310
## colData names(24): dataset subject_id ... curator BMI
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowLinks: a LinkDataFrame (189 rows)
## rowTree: 1 phylo tree(s) (10430 leaves)
## colLinks: NULL
## colTree: NULLPrior knowledge
row_data <- as.data.frame(rowData(tse))
prior_info <- row_data[, c('genus', 'taxon_annotation')]
prior_info$taxon_name <- rownames(prior_info)
prior_info$new_names <- paste0(prior_info$taxon_name, '|', prior_info$genus)
head(prior_info)## genus taxon_annotation
## Streptococcus_parasanguinis Streptococcus facultative_anaerobic
## Veillonella_dispar Veillonella anaerobic
## Veillonella_atypica Veillonella anaerobic
## Veillonella_parvula Veillonella anaerobic
## Haemophilus_parainfluenzae Haemophilus facultative_anaerobic
## Dialister_invisus Dialister anaerobic
## taxon_name
## Streptococcus_parasanguinis Streptococcus_parasanguinis
## Veillonella_dispar Veillonella_dispar
## Veillonella_atypica Veillonella_atypica
## Veillonella_parvula Veillonella_parvula
## Haemophilus_parainfluenzae Haemophilus_parainfluenzae
## Dialister_invisus Dialister_invisus
## new_names
## Streptococcus_parasanguinis Streptococcus_parasanguinis|Streptococcus
## Veillonella_dispar Veillonella_dispar|Veillonella
## Veillonella_atypica Veillonella_atypica|Veillonella
## Veillonella_parvula Veillonella_parvula|Veillonella
## Haemophilus_parainfluenzae Haemophilus_parainfluenzae|Haemophilus
## Dialister_invisus Dialister_invisus|DialisterConvert to phyloseq
ps <- makePhyloseqFromTreeSummarizedExperiment(tse)
phyloseq::sample_data(ps)$body_subsite <-
factor(phyloseq::sample_data(ps)$body_subsite)
ps## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 189 taxa and 16 samples ]
## sample_data() Sample Data: [ 16 samples by 24 sample variables ]
## tax_table() Taxonomy Table: [ 189 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 189 tips and 188 internal nodes ]Differential abundance analysis
Select methods for DA:
ps <- runNormalizations(set_norm_list(), ps, verbose = FALSE)
zw <- weights_ZINB(ps, design = conditions_col)
DA_methods <- set_DA_methods_list(conditions_col, conditions)
for (i in seq_along(DA_methods)) {
if (grepl("Seurat", names(DA_methods)[i])) {
names(DA_methods[[i]]$contrast) <- NULL
} else {
next
}
}
# These methods throw an error, so they must be removed
# DA_methods <- DA_methods[!names(DA_methods) == 'DA_ALDEx2.1']
# DA_methods <- DA_methods[!names(DA_methods) == 'DA_corncob.1']
DA_methods <- DA_methods[!names(DA_methods) == 'DA_edgeR.1']
names(DA_methods)## [1] "DA_DESeq2.1" "DA_DESeq2.1" "DA_limma.1"
## [4] "DA_limma.1" "DA_metagenomeSeq.1" "DA_ALDEx2.1"
## [7] "DA_MAST.1" "DA_Seurat.1" "ancombc.1"
## [10] "wilcox.3" "wilcox.4" "ZINQ.9"
## [13] "ZINQ.10" "lefse.12" "lefse.13"
tim <- system.time({
DA_output <- vector("list", length(DA_methods))
for (i in seq_along(DA_output)) {
message(
"Running method ", i, ": ", names(DA_methods)[i], " - ", Sys.time()
)
DA_output[[i]] <- tryCatch(
error = function(e) NULL,
runDA(DA_methods[i], ps, weights = zw, verbose = FALSE)
)
}
DA_output <- purrr::list_flatten(DA_output, name_spec = "{inner}")
DA_output <- purrr::discard(DA_output, is.null)
})## Running method 1: DA_DESeq2.1 - 2024-09-24 18:47:48.480857## Running method 2: DA_DESeq2.1 - 2024-09-24 18:47:52.812213## Running method 3: DA_limma.1 - 2024-09-24 18:47:58.303664## Running method 4: DA_limma.1 - 2024-09-24 18:47:58.327786## Running method 5: DA_metagenomeSeq.1 - 2024-09-24 18:47:58.34467## Running method 6: DA_ALDEx2.1 - 2024-09-24 18:47:58.856027## Running method 7: DA_MAST.1 - 2024-09-24 18:48:01.70039## Running method 8: DA_Seurat.1 - 2024-09-24 18:48:03.002906## For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
## (default method for FindMarkers) please install the presto package
## --------------------------------------------
## install.packages('devtools')
## devtools::install_github('immunogenomics/presto')
## --------------------------------------------
## After installation of presto, Seurat will automatically use the more
## efficient implementation (no further action necessary).
## This message will be shown once per session## Running method 9: ancombc.1 - 2024-09-24 18:48:03.490113## 'ancombc' has been fully evolved to 'ancombc2'.
## Explore the enhanced capabilities of our refined method!## Loading required package: foreach##
## Attaching package: 'foreach'## The following objects are masked from 'package:purrr':
##
## accumulate, when## Loading required package: rngtools## Running method 10: wilcox.3 - 2024-09-24 18:48:27.095663## Running method 11: wilcox.4 - 2024-09-24 18:48:27.339187## Running method 12: ZINQ.9 - 2024-09-24 18:48:27.471478## Running method 13: ZINQ.10 - 2024-09-24 18:48:28.946427## Running method 14: lefse.12 - 2024-09-24 18:48:30.182058## Running lefse original## The outcome variable is specified as 'body_subsite' and the reference category is 'subgingival_plaque'.
## See `?factor` or `?relevel` to change the reference category.## Running method 15: lefse.13 - 2024-09-24 18:48:30.594221## Running lefse original## The outcome variable is specified as 'body_subsite' and the reference category is 'subgingival_plaque'.
## See `?factor` or `?relevel` to change the reference category.
tim## user system elapsed
## 43.113 4.446 42.533Enrichment
Get direction
direction <- get_direction_cols(DA_output, conditions_col, conditions)Enrichment (adjP <= 0.1)
enrichment <- createEnrichment(
object = DA_output,
priorKnowledge = prior_info,
enrichmentCol = "taxon_annotation",
namesCol = "taxon_name",
slot = "pValMat", colName = "adjP", type = "pvalue",
direction = direction,
threshold_pvalue = 0.1,
threshold_logfc = 0,
top = NULL, # No top feature selected
alternative = "greater",
verbose = FALSE
)Plot enrichment
enrich_plot <- plot_enrichment(
enrichment = enrichment,
enrichment_col = "taxon_annotation",
levels_to_plot = c("aerobic", "anaerobic", "facultative_anaerobic"),
conditions = conditions
)
enrich_plot2 <- plot_enrichment_2(
enrich_plot,
dir = c(up = 'Sup Plq', down = 'Sub Plq')
)
enrich_plot2
Putative true positives - putative false positives
Calculate TP - FP ratio (no threshold)
positives <- createPositives(
object = DA_output,
priorKnowledge = prior_info,
enrichmentCol = "taxon_annotation", namesCol = "taxon_name",
slot = "pValMat", colName = "rawP", type = "pvalue",
direction = direction,
threshold_pvalue = 1,
threshold_logfc = 0,
top = seq.int(from = 0, to = 50, by = 5),
alternative = "greater",
verbose = FALSE,
TP = list(c("DOWN Abundant", "anaerobic"), c("UP Abundant", "aerobic")),
FP = list(c("DOWN Abundant", "aerobic"), c("UP Abundant", "anaerobic"))
) |>
left_join(get_meth_class(), by = 'method')Plot TP - FP
positive_plots <- plot_positives(positives) |>
map( ~ {
.x +
theme(
axis.title = element_text(size = 17),
axis.text = element_text(size = 15),
legend.text = element_text(size = 13),
strip.text = element_text(size = 17)
)
})
grid.arrange(grobs = positive_plots, ncol = 3)
Session Info
sessioninfo::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.4.1 (2024-06-14)
## os Ubuntu 22.04.4 LTS
## system x86_64, linux-gnu
## ui X11
## language en
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2024-09-24
## pandoc 3.2 @ /usr/bin/ (via rmarkdown)
##
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## mgcv 1.9-1 2023-12-21 [2] CRAN (R 4.4.1)
## MGLM 0.2.1 2022-04-13 [1] RSPM (R 4.4.0)
## mia * 1.12.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## mice 3.16.0 2023-06-05 [1] RSPM (R 4.4.0)
## microbiome 1.26.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## MicrobiomeBenchmarkData * 1.6.0 2024-05-02 [1] Bioconductor 3.19 (R 4.4.1)
## MicrobiomeBenchmarkDataAnalyses * 0.99.11 2024-09-24 [1] local
## MicrobiomeStat 1.2 2024-04-01 [1] RSPM (R 4.4.0)
## mime 0.12 2021-09-28 [1] RSPM (R 4.4.0)
## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.4.0)
## minqa 1.2.8 2024-08-17 [1] RSPM (R 4.4.0)
## mitml 0.4-5 2023-03-08 [1] RSPM (R 4.4.0)
## mitools 2.4 2019-04-26 [1] RSPM (R 4.4.0)
## mixOmics 6.28.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## modeest 2.4.0 2019-11-18 [1] RSPM (R 4.4.0)
## modeltools 0.2-23 2020-03-05 [1] RSPM (R 4.4.0)
## multcomp 1.4-26 2024-07-18 [1] RSPM (R 4.4.0)
## MultiAssayExperiment * 1.30.3 2024-07-10 [1] Bioconductor 3.19 (R 4.4.1)
## multtest 2.60.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## munsell 0.5.1 2024-04-01 [1] RSPM (R 4.4.0)
## mvtnorm 1.3-1 2024-09-03 [1] RSPM (R 4.4.0)
## NADA 1.6-1.1 2020-03-22 [1] RSPM (R 4.4.0)
## nlme 3.1-165 2024-06-06 [2] RSPM (R 4.4.0)
## nloptr 2.1.1 2024-06-25 [1] RSPM (R 4.4.0)
## nnet 7.3-19 2023-05-03 [2] CRAN (R 4.4.1)
## NOISeq 2.48.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## numDeriv 2016.8-1.1 2019-06-06 [1] RSPM (R 4.4.0)
## operator.tools 1.6.3 2017-02-28 [1] RSPM (R 4.4.0)
## optparse 1.7.5 2024-04-16 [1] RSPM (R 4.4.0)
## pan 1.9 2023-12-07 [1] RSPM (R 4.4.0)
## parallelly 1.38.0 2024-07-27 [1] RSPM (R 4.4.0)
## patchwork 1.3.0 2024-09-16 [1] RSPM (R 4.4.0)
## pbapply 1.7-2 2023-06-27 [1] RSPM (R 4.4.0)
## pcaPP 2.0-5 2024-08-19 [1] RSPM (R 4.4.0)
## permute 0.9-7 2022-01-27 [1] RSPM (R 4.4.0)
## phyloseq * 1.48.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## pillar 1.9.0 2023-03-22 [1] RSPM (R 4.4.0)
## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.4.0)
## pkgdown 2.1.1 2024-09-17 [1] RSPM (R 4.4.0)
## plotly 4.10.4 2024-01-13 [1] RSPM (R 4.4.0)
## plyr 1.8.9 2023-10-02 [1] RSPM (R 4.4.0)
## png 0.1-8 2022-11-29 [1] RSPM (R 4.4.0)
## polyclip 1.10-7 2024-07-23 [1] RSPM (R 4.4.0)
## prettyunits 1.2.0 2023-09-24 [1] RSPM (R 4.4.0)
## progress 1.2.3 2023-12-06 [1] RSPM (R 4.4.0)
## progressr 0.14.0 2023-08-10 [1] RSPM (R 4.4.0)
## promises 1.3.0 2024-04-05 [1] RSPM (R 4.4.0)
## proxy 0.4-27 2022-06-09 [1] RSPM (R 4.4.0)
## purrr * 1.0.2 2023-08-10 [1] RSPM (R 4.4.0)
## quadprog 1.5-8 2019-11-20 [1] RSPM (R 4.4.0)
## quantreg 5.98 2024-05-26 [1] RSPM (R 4.4.0)
## R6 2.5.1 2021-08-19 [1] RSPM (R 4.4.0)
## ragg 1.3.3 2024-09-11 [1] RSPM (R 4.4.0)
## RANN 2.6.2 2024-08-25 [1] RSPM (R 4.4.0)
## rARPACK 0.11-0 2016-03-10 [1] RSPM (R 4.4.0)
## rbibutils 2.2.16 2023-10-25 [1] RSPM (R 4.4.0)
## RColorBrewer 1.1-3 2022-04-03 [1] RSPM (R 4.4.0)
## Rcpp 1.0.13 2024-07-17 [1] RSPM (R 4.4.0)
## RcppAnnoy 0.0.22 2024-01-23 [1] RSPM (R 4.4.0)
## RcppHNSW 0.6.0 2024-02-04 [1] RSPM (R 4.4.0)
## RcppParallel 5.1.9 2024-08-19 [1] RSPM (R 4.4.0)
## RcppZiggurat 0.1.6 2020-10-20 [1] RSPM (R 4.4.0)
## Rdpack 2.6.1 2024-08-06 [1] RSPM (R 4.4.0)
## readxl 1.4.3 2023-07-06 [1] RSPM (R 4.4.0)
## reshape2 1.4.4 2020-04-09 [1] RSPM (R 4.4.0)
## reticulate 1.39.0 2024-09-05 [1] RSPM (R 4.4.0)
## Rfast 2.1.0 2023-11-09 [1] RSPM (R 4.4.0)
## rhdf5 2.48.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## rhdf5filters 1.16.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## Rhdf5lib 1.26.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## rlang 1.1.4 2024-06-04 [1] RSPM (R 4.4.0)
## rmarkdown 2.28 2024-08-17 [1] RSPM (R 4.4.0)
## Rmpfr 0.9-5 2024-01-21 [1] RSPM (R 4.4.0)
## rmutil 1.1.10 2022-10-27 [1] RSPM (R 4.4.0)
## rngtools * 1.5.2 2021-09-20 [1] RSPM (R 4.4.0)
## robustbase 0.99-4 2024-08-19 [1] RSPM (R 4.4.0)
## ROCR 1.0-11 2020-05-02 [1] RSPM (R 4.4.0)
## rootSolve 1.8.2.4 2023-09-21 [1] RSPM (R 4.4.0)
## rpart 4.1.23 2023-12-05 [2] CRAN (R 4.4.1)
## RSpectra 0.16-2 2024-07-18 [1] RSPM (R 4.4.0)
## RSQLite 2.3.7 2024-05-27 [1] RSPM (R 4.4.0)
## rstudioapi 0.16.0 2024-03-24 [1] RSPM (R 4.4.0)
## rsvd 1.0.5 2021-04-16 [1] RSPM (R 4.4.0)
## Rtsne 0.17 2023-12-07 [1] RSPM (R 4.4.0)
## S4Arrays 1.4.1 2024-05-20 [1] Bioconductor 3.19 (R 4.4.1)
## S4Vectors * 0.42.1 2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
## sandwich 3.1-1 2024-09-15 [1] RSPM (R 4.4.0)
## sass 0.4.9 2024-03-15 [1] RSPM (R 4.4.0)
## ScaledMatrix 1.12.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## scales 1.3.0 2023-11-28 [1] RSPM (R 4.4.0)
## scater 1.32.1 2024-07-21 [1] Bioconductor 3.19 (R 4.4.1)
## scattermore 1.2 2023-06-12 [1] RSPM (R 4.4.0)
## sctransform 0.4.1 2023-10-19 [1] RSPM (R 4.4.0)
## scuttle 1.14.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.4.0)
## Seurat 5.1.0 2024-05-10 [1] RSPM (R 4.4.0)
## SeuratObject 5.0.2 2024-05-08 [1] RSPM (R 4.4.0)
## shape 1.4.6.1 2024-02-23 [1] RSPM (R 4.4.0)
## shiny 1.9.1 2024-08-01 [1] RSPM (R 4.4.0)
## SingleCellExperiment * 1.26.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## SnowballC 0.7.1 2023-04-25 [1] RSPM (R 4.4.0)
## softImpute 1.4-1 2021-05-09 [1] RSPM (R 4.4.0)
## sp 2.1-4 2024-04-30 [1] RSPM (R 4.4.0)
## spam 2.10-0 2023-10-23 [1] RSPM (R 4.4.0)
## SparseArray 1.4.8 2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
## SparseM 1.84-2 2024-07-17 [1] RSPM (R 4.4.0)
## sparseMatrixStats 1.16.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## spatial 7.3-17 2023-07-20 [2] CRAN (R 4.4.1)
## spatstat.data 3.1-2 2024-06-21 [1] RSPM (R 4.4.0)
## spatstat.explore 3.3-2 2024-08-21 [1] RSPM (R 4.4.0)
## spatstat.geom 3.3-3 2024-09-18 [1] RSPM (R 4.4.0)
## spatstat.random 3.3-2 2024-09-18 [1] RSPM (R 4.4.0)
## spatstat.sparse 3.1-0 2024-06-21 [1] RSPM (R 4.4.0)
## spatstat.univar 3.0-1 2024-09-05 [1] RSPM (R 4.4.0)
## spatstat.utils 3.1-0 2024-08-17 [1] RSPM (R 4.4.0)
## stable 1.1.6 2022-03-02 [1] RSPM (R 4.4.0)
## stabledist 0.7-2 2024-08-17 [1] RSPM (R 4.4.0)
## statip 0.2.3 2019-11-17 [1] RSPM (R 4.4.0)
## statmod 1.5.0 2023-01-06 [1] RSPM (R 4.4.0)
## stringi 1.8.4 2024-05-06 [1] RSPM (R 4.4.0)
## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.4.0)
## SummarizedExperiment * 1.34.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
## survey 4.4-2 2024-03-20 [1] RSPM (R 4.4.0)
## survival 3.7-0 2024-06-05 [2] RSPM (R 4.4.0)
## systemfonts 1.1.0 2024-05-15 [1] RSPM (R 4.4.0)
## tensor 1.5 2012-05-05 [1] RSPM (R 4.4.0)
## textshaping 0.4.0 2024-05-24 [1] RSPM (R 4.4.0)
## TH.data 1.1-2 2023-04-17 [1] RSPM (R 4.4.0)
## tibble 3.2.1 2023-03-20 [1] RSPM (R 4.4.0)
## tidyr 1.3.1 2024-01-24 [1] RSPM (R 4.4.0)
## tidyselect 1.2.1 2024-03-11 [1] RSPM (R 4.4.0)
## tidytext 0.4.2 2024-04-10 [1] RSPM (R 4.4.0)
## tidytree 0.4.6 2023-12-12 [1] RSPM (R 4.4.0)
## timeDate 4041.110 2024-09-22 [1] RSPM (R 4.4.0)
## timeSeries 4041.111 2024-09-22 [1] RSPM (R 4.4.0)
## tokenizers 0.3.0 2022-12-22 [1] RSPM (R 4.4.0)
## treeio 1.28.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## TreeSummarizedExperiment * 2.12.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## truncnorm 1.0-9 2023-03-20 [1] RSPM (R 4.4.0)
## UCSC.utils 1.0.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## utf8 1.2.4 2023-10-22 [1] RSPM (R 4.4.0)
## uwot 0.2.2 2024-04-21 [1] RSPM (R 4.4.0)
## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.4.0)
## vegan 2.6-8 2024-08-28 [1] RSPM (R 4.4.0)
## vipor 0.4.7 2023-12-18 [1] RSPM (R 4.4.0)
## viridis 0.6.5 2024-01-29 [1] RSPM (R 4.4.0)
## viridisLite 0.4.2 2023-05-02 [1] RSPM (R 4.4.0)
## withr 3.0.1 2024-07-31 [1] RSPM (R 4.4.0)
## Wrench 1.22.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## xfun 0.47 2024-08-17 [1] RSPM (R 4.4.0)
## XML 3.99-0.17 2024-06-25 [1] RSPM (R 4.4.0)
## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.4.0)
## XVector * 0.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## yaml 2.3.10 2024-07-26 [1] RSPM (R 4.4.0)
## yulab.utils 0.1.7 2024-08-26 [1] RSPM (R 4.4.0)
## zCompositions 1.5.0-4 2024-06-19 [1] RSPM (R 4.4.0)
## zinbwave 1.26.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## ZINQ 2.0 2024-09-24 [1] Github (wdl2459/ZINQ-v2@40391a6)
## zlibbioc 1.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
## zoo 1.8-12 2023-04-13 [1] RSPM (R 4.4.0)
##
## [1] /usr/local/lib/R/site-library
## [2] /usr/local/lib/R/library
##
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