## ---- eval = FALSE------------------------------------------------------------ # BiocManager::install("tuberculosis") ## ---- eval = FALSE------------------------------------------------------------ # BiocManager::install("schifferl/tuberculosis", dependencies = TRUE, build_vignettes = TRUE) ## ---- message = FALSE--------------------------------------------------------- library(tuberculosis) ## ----------------------------------------------------------------------------- tuberculosis("GSE103147") ## ----------------------------------------------------------------------------- tuberculosis("GSE103147", dryrun = FALSE) ## ----------------------------------------------------------------------------- tuberculosis("GSE10799.", dryrun = FALSE) ## ----------------------------------------------------------------------------- zak_data <- tuberculosis("GSE103147", dryrun = FALSE) |> magrittr::use_series("2021-09-15.GSE103147") ## ----------------------------------------------------------------------------- row_names <- base::colnames(zak_data) ## ----------------------------------------------------------------------------- col_names <- purrr::map_chr(1:2, ~ base::paste("UMAP", .x, sep = "")) ## ---- fig.width = 8, fig.height = 8------------------------------------------- scater::calculateUMAP(zak_data, exprs_values = "exprs") |> magrittr::set_rownames(row_names) |> magrittr::set_colnames(col_names) |> base::as.data.frame() |> ggplot2::ggplot(mapping = ggplot2::aes(UMAP1, UMAP2)) + ggplot2::geom_point() + hrbrthemes::theme_ipsum_rc() ## ----------------------------------------------------------------------------- utils::sessionInfo()