diff --git a/DESCRIPTION b/DESCRIPTION index ec15633..8498af1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Encoding: UTF-8 Type: Package Package: fastTopics -Version: 0.6-185 -Date: 2024-06-27 +Version: 0.6-186 +Date: 2024-06-28 Title: Fast Algorithms for Fitting Topic Models and Non-Negative Matrix Factorizations to Count Data Authors@R: c(person("Peter","Carbonetto",role=c("aut","cre"), diff --git a/R/fit_poisson_nmf.R b/R/fit_poisson_nmf.R index 3e853e7..75da745 100644 --- a/R/fit_poisson_nmf.R +++ b/R/fit_poisson_nmf.R @@ -449,7 +449,7 @@ fit_poisson_nmf <- function (X, k, fit0, numiter = 100, cat(sprintf("Running at most %d %s updates, %s extrapolation ", numiter,method.text, ifelse(control$extrapolate,"with","without"))) - cat("(fastTopics 0.6-185).\n") + cat("(fastTopics 0.6-186).\n") } # INITIALIZE ESTIMATES diff --git a/R/pbmc_facs.R b/R/pbmc_facs.R index 31b1634..a448b8d 100644 --- a/R/pbmc_facs.R +++ b/R/pbmc_facs.R @@ -39,14 +39,8 @@ #' #' \item{fit}{Poisson non-negative matrix factorization (NMF) fitted #' to the UMI count data \code{counts}, with rank \code{k = 6}. See -#' the vignette how the Poisson NMF model fitting was performed.} +#' the vignette how the Poisson NMF model fitting was performed.}} #' -#' \item{de}{Result of calling -#' \code{de_analysis(fit,counts,pseudocount = 0.1, -#' control = list(ns = 1e4,nc = 4))} -#' after first setting the seed to 1, \code{set.seed(1)}.}} -#' -#' @source #' \url{https://www.10xgenomics.com/resources/datasets} #' #' @references diff --git a/data/pbmc_facs.RData b/data/pbmc_facs.RData index fbddbd5..6fb7c42 100644 Binary files a/data/pbmc_facs.RData and b/data/pbmc_facs.RData differ diff --git a/man/pbmc_facs.Rd b/man/pbmc_facs.Rd index 19896df..5fad738 100644 --- a/man/pbmc_facs.Rd +++ b/man/pbmc_facs.Rd @@ -28,14 +28,8 @@ \item{fit}{Poisson non-negative matrix factorization (NMF) fitted to the UMI count data \code{counts}, with rank \code{k = 6}. See - the vignette how the Poisson NMF model fitting was performed.} + the vignette how the Poisson NMF model fitting was performed.}} - \item{de}{Result of calling - \code{de_analysis(fit,counts,pseudocount = 0.1, - control = list(ns = 1e4,nc = 4))} - after first setting the seed to 1, \code{set.seed(1)}.}} -} -\source{ \url{https://www.10xgenomics.com/resources/datasets} } \description{ diff --git a/vignettes/single_cell_rnaseq_basic.Rmd b/vignettes/single_cell_rnaseq_basic.Rmd index 9bc10b1..53c3c5e 100644 --- a/vignettes/single_cell_rnaseq_basic.Rmd +++ b/vignettes/single_cell_rnaseq_basic.Rmd @@ -268,9 +268,14 @@ de <- de_analysis(fit,counts,pseudocount = 0.1, Since this computation can take 10 minutes or more to run, we have provided the output of this `de_analysis` call in the `pbmc_facs` data -set: +set. Since the `de_analysis` output is quite large, we have made this +available outside the package: ```{r de-analysis-2} +pbmc_facs_file <- tempfile(fileext = ".RData") +pbmc_facs_url <- "https://stephenslab.github.io/fastTopics/pbmc_facs.RData" +download.file(pbmc_facs_url,pbmc_facs_file) +load(pbmc_facs_file) de <- pbmc_facs$de ``` diff --git a/vignettes/single_cell_rnaseq_practical.Rmd b/vignettes/single_cell_rnaseq_practical.Rmd index aea4bd1..db1f7d9 100644 --- a/vignettes/single_cell_rnaseq_practical.Rmd +++ b/vignettes/single_cell_rnaseq_practical.Rmd @@ -194,10 +194,15 @@ More on differential expression analysis ---------------------------------------- In [Part 1][vignette-part-1], we performed a DE analysis using the -topic model. +topic model. (Note that since the `de_analysis` output is quite large, +we have made the results of the DE analysis available outside the +package.) ```{r diff-count-analysis} -de <- pbmc_facs$de +pbmc_facs_file <- tempfile(fileext = ".RData") +pbmc_facs_url <- "https://stephenslab.github.io/fastTopics/pbmc_facs.RData" +download.file(pbmc_facs_url,pbmc_facs_file) +load(pbmc_facs_file) ``` When the volcano plot shows many overlapping differentially expressed