## ----include = FALSE---------------------------------------------------------- library(curatedMetagenomicData) ## ----eval = FALSE------------------------------------------------------------- # BiocManager::install("curatedMetagenomicData") ## ----eval = FALSE------------------------------------------------------------- # BiocManager::install("waldronlab/curatedMetagenomicData", dependencies = TRUE, build_vignettes = TRUE) ## ----message = FALSE---------------------------------------------------------- library(dplyr) library(DT) ## ----collapse = TRUE---------------------------------------------------------- sampleMetadata |> filter(study_name == "AsnicarF_2017") |> select(where(~ !any(is.na(.x)))) |> slice(1:10) |> select(1:10) |> datatable(options = list(dom = "t"), extensions = "Responsive") ## ----collapse = TRUE---------------------------------------------------------- curatedMetagenomicData("AsnicarF_20.+") ## ----collapse = TRUE, message = FALSE----------------------------------------- curatedMetagenomicData("AsnicarF_2017.relative_abundance", dryrun = FALSE, rownames = "short") ## ----collapse = TRUE, message = FALSE----------------------------------------- curatedMetagenomicData("AsnicarF_20.+.relative_abundance", dryrun = FALSE, counts = TRUE, rownames = "short") ## ----collapse = TRUE, message = FALSE----------------------------------------- curatedMetagenomicData("AsnicarF_20.+.marker_abundance", dryrun = FALSE) |> mergeData() ## ----collapse = TRUE, message = FALSE----------------------------------------- curatedMetagenomicData("AsnicarF_20.+.pathway_abundance", dryrun = FALSE) |> mergeData() ## ----collapse = TRUE, message = FALSE----------------------------------------- curatedMetagenomicData("AsnicarF_20.+.relative_abundance", dryrun = FALSE, rownames = "short") |> mergeData() ## ----collapse = TRUE, message = FALSE----------------------------------------- sampleMetadata |> filter(age >= 18) |> filter(!is.na(alcohol)) |> filter(body_site == "stool") |> select(where(~ !all(is.na(.x)))) |> returnSamples("relative_abundance", rownames = "short") ## ----message = FALSE---------------------------------------------------------- library(stringr) library(mia) library(scater) library(vegan) ## ----collapse = TRUE, message = FALSE----------------------------------------- alcoholStudy <- filter(sampleMetadata, age >= 18) |> filter(!is.na(alcohol)) |> filter(body_site == "stool") |> select(where(~ !all(is.na(.x)))) |> returnSamples("relative_abundance", rownames = "short") ## ----collapse = TRUE, message = FALSE----------------------------------------- colData(alcoholStudy) <- colData(alcoholStudy) |> as.data.frame() |> mutate(alcohol = str_replace_all(alcohol, "no", "No")) |> mutate(alcohol = str_replace_all(alcohol, "yes", "Yes")) |> DataFrame() ## ----collapse = TRUE, message = FALSE----------------------------------------- altExps(alcoholStudy) <- splitByRanks(alcoholStudy) ## ----collapse = TRUE, fig.cap = "Alpha Diversity – Shannon Index (H')"-------- alcoholStudy |> estimateDiversity(assay.type = "relative_abundance", index = "shannon") |> plotColData(x = "alcohol", y = "shannon", colour_by = "alcohol", shape_by = "alcohol") + labs(x = "Alcohol", y = "Alpha Diversity (H')") + guides(colour = guide_legend(title = "Alcohol"), shape = guide_legend(title = "Alcohol")) + theme(legend.position = "none") ## ----collapse = TRUE, fig.cap = "Beta Diversity – Bray–Curtis PCoA"----------- alcoholStudy |> runMDS(FUN = vegdist, method = "bray", exprs_values = "relative_abundance", altexp = "genus", name = "BrayCurtis") |> plotReducedDim("BrayCurtis", colour_by = "alcohol", shape_by = "alcohol") + labs(x = "PCo 1", y = "PCo 2") + guides(colour = guide_legend(title = "Alcohol"), shape = guide_legend(title = "Alcohol")) + theme(legend.position = c(0.90, 0.85)) ## ----collapse = TRUE, fig.cap = "Beta Diversity – UMAP (Uniform Manifold Approximation and Projection)"---- alcoholStudy |> runUMAP(exprs_values = "relative_abundance", altexp = "genus", name = "UMAP") |> plotReducedDim("UMAP", colour_by = "alcohol", shape_by = "alcohol") + labs(x = "UMAP 1", y = "UMAP 2") + guides(colour = guide_legend(title = "Alcohol"), shape = guide_legend(title = "Alcohol")) + theme(legend.position = c(0.90, 0.85)) ## ----eval = FALSE------------------------------------------------------------- # makePhyloseqFromTreeSummarizedExperiment(alcoholStudy, abund_values = "relative_abundance") ## ----echo = FALSE------------------------------------------------------------- utils::sessionInfo()