From 3317b2cad6a80c6316c579b48f86b76c401b789d Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Thu, 27 Nov 2025 17:07:51 +0100 Subject: [PATCH 1/4] retrieving gmt file from a more up to date version of wikipathways --- R/CIA_core.R | 2 +- man/load_signatures.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/CIA_core.R b/R/CIA_core.R index 2ced7a0..2719722 100644 --- a/R/CIA_core.R +++ b/R/CIA_core.R @@ -26,7 +26,7 @@ #' signatures #' #' gmt_url <- -#' "https://data.wikipathways.org/20240710/gmt/wikipathways-20240710-gmt-Homo_sapiens.gmt" +#' "https://data.wikipathways.org/20251110/gmt/wikipathways-20251110-gmt-Homo_sapiens.gmt" #' #' sig_wikipathways <- load_signatures(gmt_url) #' head(names(sig_wikipathways)) diff --git a/man/load_signatures.Rd b/man/load_signatures.Rd index f742f64..4dc0269 100644 --- a/man/load_signatures.Rd +++ b/man/load_signatures.Rd @@ -31,7 +31,7 @@ signatures <- load_signatures(gmt_file) signatures gmt_url <- - "https://data.wikipathways.org/20240710/gmt/wikipathways-20240710-gmt-Homo_sapiens.gmt" + "https://data.wikipathways.org/20251110/gmt/wikipathways-20251110-gmt-Homo_sapiens.gmt" sig_wikipathways <- load_signatures(gmt_url) head(names(sig_wikipathways)) From 20b9319be606bc76564e3e66fd3df426151a0b45 Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Thu, 27 Nov 2025 17:08:01 +0100 Subject: [PATCH 2/4] bumped version of roxygen --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 447fabf..819a9ba 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,7 @@ Description: CIA (Cluster Independent Annotation) is designed to accurately License: MIT + file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Imports: SingleCellExperiment, SummarizedExperiment, From 5170c9f32def8a770b957f4a315ea4b0e189d1bd Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Thu, 27 Nov 2025 17:08:22 +0100 Subject: [PATCH 3/4] bump also package version number for completeness --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 819a9ba..0456014 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: CIA Title: Cluster Independent Annotation (CIA) to Accurately Classify Cells in scRNA-seq Datasets Using Gene Signatures -Version: 0.3.0 +Version: 0.3.1 Authors@R: c( person( From 197383a458f04551b65d482b75f2fcf205464c23 Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Thu, 27 Nov 2025 17:55:16 +0100 Subject: [PATCH 4/4] swapping the labels of the axes for grouped_distributions() --- R/CIA_metrics.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/CIA_metrics.R b/R/CIA_metrics.R index 4d09529..cffb992 100644 --- a/R/CIA_metrics.R +++ b/R/CIA_metrics.R @@ -584,8 +584,8 @@ grouped_distributions <- function(data, theme_minimal() + labs( title = "Median score values", - x = "Signatures", - y = ref_obs + x = ref_obs, + y = "Signatures" ) ## Save or display plot