From ac216c364b09da8d8e39b08df99984c7d4a89040 Mon Sep 17 00:00:00 2001 From: antagomir Date: Mon, 23 Mar 2026 09:01:36 +0200 Subject: [PATCH 1/3] Extended author info for JointRPCA --- R/getRPCA.R | 11 +++++++++++ man/getRPCA.Rd | 11 +++++++++++ 2 files changed, 22 insertions(+) diff --git a/R/getRPCA.R b/R/getRPCA.R index e608e97c2..ed25334f7 100644 --- a/R/getRPCA.R +++ b/R/getRPCA.R @@ -110,6 +110,17 @@ #' @seealso #' \code{\link[scater:runPCA]{scater::runPCA}} #' +#' @author +#' The RPCA method is reported in Martino et al. (2020) and the +#' R/Bioconductor implementation utilizes the robust Aitchison +#' distance from \code{\link[vegan:decostand]{vegan::decostand}}. +#' +#' The Joint-RPCA method was adapted from the original +#' Python-based implementation in biocore/Gemelli by +#' Bianca Cordazzo Vargas, Liat Shenhav, and Cameron Martino. +#' The R/Bioconductor implementation was subsequently prepared by +#' Aituar Bektanov, Tuomas Borman, and Leo Lahti. +#' #' @references #' #' Martino, C. and Shenhav, L. et al. (2020) diff --git a/man/getRPCA.Rd b/man/getRPCA.Rd index 17263e4d8..d7b036a29 100644 --- a/man/getRPCA.Rd +++ b/man/getRPCA.Rd @@ -149,3 +149,14 @@ dynamics. \seealso{ \code{\link[scater:runPCA]{scater::runPCA}} } +\author{ +The RPCA method is reported in Martino et al. (2020) and the +R/Bioconductor implementation utilizes the robust Aitchison +distance from \code{\link[vegan:decostand]{vegan::decostand}}. + +The Joint-RPCA method was adapted from the original +Python-based implementation in biocore/Gemelli by +Bianca Cordazzo Vargas, Liat Shenhav, and Cameron Martino. +The R/Bioconductor implementation was subsequently prepared by +Aituar Bektanov, Tuomas Borman, and Leo Lahti. +} From aa63b215f373c25cab80e68e5d15433b42f50290 Mon Sep 17 00:00:00 2001 From: antagomir Date: Mon, 23 Mar 2026 18:16:05 +0200 Subject: [PATCH 2/3] pseudocount message refined --- R/transformCounts.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/transformCounts.R b/R/transformCounts.R index 8ae315fdf..abb4e6e14 100644 --- a/R/transformCounts.R +++ b/R/transformCounts.R @@ -687,7 +687,9 @@ setMethod("transformAssay", signature = c(x = "SingleCellExperiment"), if( pseudocount && all(mat > 0, na.rm = TRUE) ){ pseudocount <- 0 message("The assay contains already only strictly positive ", - "values. Pseudocount is not added.") + "values. It is not recommended to add pseudocount", + "in such case. To force adding pseudocount you can", + "provide a numeric value for the pseudocount argument.") } # If pseudocount TRUE, set it to half of non-zero minimum value # else set it to zero. From f1f7c66031b1a0cbea0561fe7a79bb3acf830937 Mon Sep 17 00:00:00 2001 From: antagomir Date: Mon, 23 Mar 2026 18:16:36 +0200 Subject: [PATCH 3/3] pseudocount message refined --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 38bceae30..a6477e256 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: mia Type: Package -Version: 1.19.6 +Version: 1.19.7 Authors@R: c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"), email = "tuomas.v.borman@utu.fi",