HMP_2012_16S_gingival_V35_subset - subgingival vs supragingival
Source:vignettes/articles/HMP_2012_16S_gingival_V35_subset.Rmd
HMP_2012_16S_gingival_V35_subset.Rmd
library(MicrobiomeBenchmarkDataAnalyses)
library(MicrobiomeBenchmarkData)
library(mia)
library(benchdamic)
library(dplyr)
library(ggplot2)
library(gridExtra)
library(purrr)Import data
dat_name <-'HMP_2012_16S_gingival_V35_subset'
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: 783 76
## metadata(0):
## assays(1): counts
## rownames(783): OTU_97.31247 OTU_97.44487 ... OTU_97.45365 OTU_97.45307
## rowData names(7): kingdom phylum ... genus taxon_annotation
## colnames(76): 700023057 700023179 ... 700114009 700114338
## colData names(13): dataset subject_id ... sequencing_method
## variable_region_16s
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowLinks: a LinkDataFrame (783 rows)
## rowTree: 1 phylo tree(s) (892 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 taxon_name
## OTU_97.31247 Streptococcus facultative_anaerobic OTU_97.31247
## OTU_97.44487 Streptococcus facultative_anaerobic OTU_97.44487
## OTU_97.34979 Streptococcus facultative_anaerobic OTU_97.34979
## OTU_97.34572 Streptococcus facultative_anaerobic OTU_97.34572
## OTU_97.42259 Streptococcus facultative_anaerobic OTU_97.42259
## OTU_97.34698 Streptococcus facultative_anaerobic OTU_97.34698
## new_names
## OTU_97.31247 OTU_97.31247|Streptococcus
## OTU_97.44487 OTU_97.44487|Streptococcus
## OTU_97.34979 OTU_97.34979|Streptococcus
## OTU_97.34572 OTU_97.34572|Streptococcus
## OTU_97.42259 OTU_97.42259|Streptococcus
## OTU_97.34698 OTU_97.34698|StreptococcusConvert 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: [ 783 taxa and 76 samples ]
## sample_data() Sample Data: [ 76 samples by 13 sample variables ]
## tax_table() Taxonomy Table: [ 783 taxa by 6 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 783 tips and 778 internal nodes ]Run 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
}
}
names(DA_methods)## [1] "DA_edgeR.1" "DA_edgeR.1" "DA_DESeq2.1"
## [4] "DA_DESeq2.1" "DA_limma.1" "DA_limma.1"
## [7] "DA_metagenomeSeq.1" "DA_ALDEx2.1" "DA_MAST.1"
## [10] "DA_Seurat.1" "ancombc.1" "wilcox.3"
## [13] "wilcox.4" "ZINQ.9" "ZINQ.10"
## [16] "lefse.12" "lefse.13"Run all of the differential analysis (DA) methods:
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)
})
tim## user system elapsed
## 118.330 2.988 118.159Enrichment
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 = "new_names",
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 = c(condB = 'subgingival', condA = 'supragingival')
)
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 = "new_names",
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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## 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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