From 511c30406e64bd3d8777786bbf1b9139ed6defbb Mon Sep 17 00:00:00 2001 From: George Chen <72078254+jiajic@users.noreply.github.com> Date: Sun, 11 Aug 2024 21:14:10 -0400 Subject: [PATCH 1/3] docs updates --- R/convenience_visiumHD.R | 2 +- R/feature_set_enrichment.R | 2 +- man/doFeatureSetEnrichment.Rd | 2 +- man/importVisiumHD.Rd | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/convenience_visiumHD.R b/R/convenience_visiumHD.R index 1f8178665..a0c3ca5fe 100644 --- a/R/convenience_visiumHD.R +++ b/R/convenience_visiumHD.R @@ -138,7 +138,7 @@ setMethod("print", signature("VisiumHDReader"), function(x, ...) show(x)) #' array_subset_col = c(500, 1000)) #' #' # Create a `giotto` object and add the loaded data -#' TODO +#' # TODO #' } #' @export importVisiumHD <- function( diff --git a/R/feature_set_enrichment.R b/R/feature_set_enrichment.R index c5bf382ea..8bb2568cb 100644 --- a/R/feature_set_enrichment.R +++ b/R/feature_set_enrichment.R @@ -46,7 +46,7 @@ #' for more details, see: #' https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#RNK:_Ranked_list_file_format_.28.2A.rnk.29 #' -#' For more information on parameter convetions, +#' For more information on parameter conventions, #' please reference GSEA's documentation here: #' https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Syntax #' @export diff --git a/man/doFeatureSetEnrichment.Rd b/man/doFeatureSetEnrichment.Rd index 359b7d3e5..470e47dbd 100644 --- a/man/doFeatureSetEnrichment.Rd +++ b/man/doFeatureSetEnrichment.Rd @@ -87,7 +87,7 @@ column 1 = gene symbols, column 2 = weight or rank metric for more details, see: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#RNK:_Ranked_list_file_format_.28.2A.rnk.29 -For more information on parameter convetions, +For more information on parameter conventions, please reference GSEA's documentation here: https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Syntax } diff --git a/man/importVisiumHD.Rd b/man/importVisiumHD.Rd index 08fb3801b..cf54b664c 100644 --- a/man/importVisiumHD.Rd +++ b/man/importVisiumHD.Rd @@ -76,6 +76,6 @@ my_transcripts = readerHD$load_transcripts(array_subset_row = c(500, 1000), array_subset_col = c(500, 1000)) # Create a `giotto` object and add the loaded data -TODO +# TODO } } From 04ec7362f6dae0bdb19e269e418b7959049ab0ef Mon Sep 17 00:00:00 2001 From: George Chen <72078254+jiajic@users.noreply.github.com> Date: Tue, 13 Aug 2024 05:06:02 -0400 Subject: [PATCH 2/3] fix: allow instructions passing for Xenium conv. --- R/convenience_xenium.R | 9 +++++++-- man/createGiottoXeniumObject.Rd | 6 +++++- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R index ef7f9d836..e8b437286 100644 --- a/R/convenience_xenium.R +++ b/R/convenience_xenium.R @@ -373,6 +373,7 @@ setMethod( load_aligned_images = NULL, load_expression = FALSE, load_cellmeta = FALSE, + instructions = NULL, verbose = NULL ) { load_expression <- as.logical(load_expression) @@ -413,7 +414,7 @@ setMethod( funs <- obj@calls # init gobject - g <- giotto() + g <- giotto(instructions = instructions) # transcripts @@ -1215,8 +1216,10 @@ importXenium <- function( #' slower in our imaging pipeline. #' @param load_expression logical. Default = FALSE. Whether to load in 10X #' provided expression matrix. -#' @param load_cellmeta logical. Default = FALSE. Whether to laod in 10X +#' @param load_cellmeta logical. Default = FALSE. Whether to load in 10X #' provided cell metadata information +#' @param instructions list of instructions or output result from +#' [createGiottoInstructions()] #' @param verbose logical or NULL. NULL uses the `giotto.verbose` option #' setting and defaults to TRUE. #' @returns `giotto` object @@ -1282,6 +1285,7 @@ createGiottoXeniumObject <- function( load_aligned_images = NULL, load_expression = FALSE, load_cellmeta = FALSE, + instructions = NULL, verbose = NULL ) { x <- importXenium(xenium_dir) @@ -1296,6 +1300,7 @@ createGiottoXeniumObject <- function( load_aligned_images = load_aligned_images, load_expression = load_expression, load_cellmeta = load_cellmeta, + instructions = instructions, verbose = verbose) # only passed if not null diff --git a/man/createGiottoXeniumObject.Rd b/man/createGiottoXeniumObject.Rd index 0d310af52..f803aece8 100644 --- a/man/createGiottoXeniumObject.Rd +++ b/man/createGiottoXeniumObject.Rd @@ -18,6 +18,7 @@ createGiottoXeniumObject( load_aligned_images = NULL, load_expression = FALSE, load_cellmeta = FALSE, + instructions = NULL, verbose = NULL ) } @@ -68,9 +69,12 @@ slower in our imaging pipeline.} \item{load_expression}{logical. Default = FALSE. Whether to load in 10X provided expression matrix.} -\item{load_cellmeta}{logical. Default = FALSE. Whether to laod in 10X +\item{load_cellmeta}{logical. Default = FALSE. Whether to load in 10X provided cell metadata information} +\item{instructions}{list of instructions or output result from +\code{\link[=createGiottoInstructions]{createGiottoInstructions()}}} + \item{verbose}{logical or NULL. NULL uses the \code{giotto.verbose} option setting and defaults to TRUE.} } From 26bedbd64489b44689cc2c0b7e999fb9736562fc Mon Sep 17 00:00:00 2001 From: George Chen <72078254+jiajic@users.noreply.github.com> Date: Tue, 13 Aug 2024 05:07:49 -0400 Subject: [PATCH 3/3] chore: bump version and update news --- DESCRIPTION | 2 +- NEWS.md | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 945224e9a..2274bef4f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Giotto Title: Spatial Single-Cell Transcriptomics Toolbox -Version: 4.1.0 +Version: 4.1.1 Authors@R: c( person("Ruben", "Dries", email = "rubendries@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")), diff --git a/NEWS.md b/NEWS.md index 9d8438301..5269365d9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ + +# Giotto 4.1.1 + +## Bug fixes +* Allow `giottoInstructions` passing for Xenium convenience functions + + # Giotto 4.1.0 (2024/07/31) ## Breaking changes