From 15670e707b0c8b711935a7a873bc2adf850d33e0 Mon Sep 17 00:00:00 2001 From: Nitesh Turaga Date: Tue, 26 Oct 2021 16:49:54 +0000 Subject: [PATCH 01/16] bump x.y.z version to even y prior to creation of RELEASE_3_14 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 33a13be..bea5581 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.9.1 +Version: 1.10.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Stefano", family="Monti", email="smonti@bu.edu", From fb28216fb13d213e30f258b4be673494cdcc6f3e Mon Sep 17 00:00:00 2001 From: Nitesh Turaga Date: Tue, 26 Oct 2021 16:49:54 +0000 Subject: [PATCH 02/16] bump x.y.z version to odd y following creation of RELEASE_3_14 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index bea5581..e6f7f66 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.10.0 +Version: 1.11.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Stefano", family="Monti", email="smonti@bu.edu", From be72ad016f5dccc256e91f14ea20d4545c56a096 Mon Sep 17 00:00:00 2001 From: Nitesh Turaga Date: Tue, 26 Apr 2022 15:53:35 +0000 Subject: [PATCH 03/16] bump x.y.z version to even y prior to creation of RELEASE_3_15 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index e6f7f66..e26b2f6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.11.0 +Version: 1.12.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Stefano", family="Monti", email="smonti@bu.edu", From bb36ba4769fa6b1c73fa4279310c770741ac04f8 Mon Sep 17 00:00:00 2001 From: Nitesh Turaga Date: Tue, 26 Apr 2022 15:53:35 +0000 Subject: [PATCH 04/16] bump x.y.z version to odd y following creation of RELEASE_3_15 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index e26b2f6..407f727 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.12.0 +Version: 1.13.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Stefano", family="Monti", email="smonti@bu.edu", From 8787f212f82d3c861db6f52e58c08293bdd27daa Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 1 Nov 2022 11:19:22 -0400 Subject: [PATCH 05/16] bump x.y.z version to even y prior to creation of RELEASE_3_16 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 407f727..fb6e897 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.13.0 +Version: 1.14.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Stefano", family="Monti", email="smonti@bu.edu", From c177f48423ba9b954968523b0cf0b2ff5e894467 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 1 Nov 2022 11:19:22 -0400 Subject: [PATCH 06/16] bump x.y.z version to odd y following creation of RELEASE_3_16 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index fb6e897..690bafd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.14.0 +Version: 1.15.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Stefano", family="Monti", email="smonti@bu.edu", From b25ccb4188a04af71a248aae8c508f6deab48eca Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 25 Apr 2023 11:08:22 -0400 Subject: [PATCH 07/16] bump x.y.z version to even y prior to creation of RELEASE_3_17 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 690bafd..be123e3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.15.0 +Version: 1.16.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Stefano", family="Monti", email="smonti@bu.edu", From bdeeb2329a74f5b17dfac0317838fe60c476cd24 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 25 Apr 2023 11:08:22 -0400 Subject: [PATCH 08/16] bump x.y.z version to odd y following creation of RELEASE_3_17 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index be123e3..31e68b9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.16.0 +Version: 1.17.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Stefano", family="Monti", email="smonti@bu.edu", From 52a51c11967d4f9690b0b57eb73fc76d90899f43 Mon Sep 17 00:00:00 2001 From: lshep Date: Tue, 27 Jun 2023 08:51:38 -0400 Subject: [PATCH 09/16] Deprecated - unresponsive --- DESCRIPTION | 3 ++- R/zzz.R | 7 +++++++ 2 files changed, 9 insertions(+), 1 deletion(-) create mode 100644 R/zzz.R diff --git a/DESCRIPTION b/DESCRIPTION index 31e68b9..9196045 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.17.0 +Version: 1.17.1 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Stefano", family="Monti", email="smonti@bu.edu", @@ -42,3 +42,4 @@ Suggests: biocViews: GeneSetEnrichment, Annotation, Pathways VignetteBuilder: knitr BugReports: https://github.com/montilab/hypeR/issues +PackageStatus: Deprecated diff --git a/R/zzz.R b/R/zzz.R new file mode 100644 index 0000000..1cda9f2 --- /dev/null +++ b/R/zzz.R @@ -0,0 +1,7 @@ +.onAttach <- function(libname, pkgname) { + msg <- sprintf( + "Package '%s' is deprecated and will be removed from Bioconductor + version %s", pkgname, "3.19") + .Deprecated(msg=paste(strwrap(msg, exdent=2), collapse="\n")) +} + From cca2a5a925b18b838dda35861122a39de616903c Mon Sep 17 00:00:00 2001 From: anfederico Date: Tue, 17 Oct 2023 19:59:36 -0400 Subject: [PATCH 10/16] Bump for bioc --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index e0124d7..1443221 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 2.0.1 +Version: 2.1.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Andrew", family="Chen", email="andrewdr@bu.edu", From be7e3c981b3e8e2c1f1ef1ea703d53b00152a88a Mon Sep 17 00:00:00 2001 From: anfederico Date: Tue, 17 Oct 2023 20:02:01 -0400 Subject: [PATCH 11/16] Delete zzz.R --- R/zzz.R | 7 ------- 1 file changed, 7 deletions(-) delete mode 100644 R/zzz.R diff --git a/R/zzz.R b/R/zzz.R deleted file mode 100644 index 1cda9f2..0000000 --- a/R/zzz.R +++ /dev/null @@ -1,7 +0,0 @@ -.onAttach <- function(libname, pkgname) { - msg <- sprintf( - "Package '%s' is deprecated and will be removed from Bioconductor - version %s", pkgname, "3.19") - .Deprecated(msg=paste(strwrap(msg, exdent=2), collapse="\n")) -} - From badbb7b32f78c60e9b3372bc546afab1886d3457 Mon Sep 17 00:00:00 2001 From: anfederico Date: Tue, 17 Oct 2023 21:20:26 -0400 Subject: [PATCH 12/16] Signify major change --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1443221..0697d53 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 2.1.0 +Version: 1.99.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Andrew", family="Chen", email="andrewdr@bu.edu", From dfcd960f4fcbc005ecc9f39714d187ddd77d4102 Mon Sep 17 00:00:00 2001 From: tetomonti Date: Fri, 20 Oct 2023 17:40:25 -0400 Subject: [PATCH 13/16] fixed dotplot by genesetsize --- R/hyp_dots.R | 34 ++++++++++++++++++++++++---------- 1 file changed, 24 insertions(+), 10 deletions(-) diff --git a/R/hyp_dots.R b/R/hyp_dots.R index 642152c..383e70a 100644 --- a/R/hyp_dots.R +++ b/R/hyp_dots.R @@ -20,7 +20,7 @@ .dots_multi_plot <- function(multihyp_data, top=20, abrv=50, - size_by=c("genesets", "significance", "none"), + size_by=c("genesets", "significance", "overlap", "none"), pval_cutoff=1, fdr_cutoff=1, val=c("fdr", "pval"), @@ -79,16 +79,29 @@ if (size_by == "significance") { df.melted$size <- df.melted$significance - } - - if (size_by == "genesets") { + } else if (size_by == "genesets") { geneset.sizes <- lapply(multihyp_data, function(hyp_obj) { hyp_obj$data[, c("label", "geneset")] }) %>% do.call(rbind, .) %>% dplyr::distinct(label, .keep_all=TRUE) %>% dplyr::pull(geneset, label) - df.melted$size <- geneset.sizes[df.melted$label] + #df.melted$size <- geneset.sizes[df.melted$label] + names(geneset.sizes) <- substr(names(geneset.sizes), 1, abrv) + stopifnot( all(!is.na(match_idx <- match(df.melted$label,names(geneset.sizes)))) ) + df.melted$size <- geneset.sizes[match_idx] + } else if (size == "overlap") { + stop( "size_by overlap not implemented yet") + overlap.sizes <- lapply(multihyp_data, function(hyp_obj) { + hyp_obj$data[, c("label", "overlap")] + }) %>% + do.call(rbind, .) %>% + dplyr::distinct(label, .keep_all=TRUE) %>% + dplyr::pull(overlap, label) + #df.melted$size <- overlap.sizes[df.melted$label] + names(overlap.sizes) <- substr(names(overlap.sizes), 1, abrv) + stopifnot( all(!is.na(match_idx <- match(df.melted$label,names(overlap.sizes)))) ) + df.melted$size <- overlap.sizes[match_idx] } p <- df.melted %>% @@ -104,14 +117,15 @@ if (size_by == "none") { p <- p + guides(size="none") - } - if (size_by == "significance") { + } else if (size_by == "significance") { p <- p + scale_size_continuous(trans=.reverselog_trans(10)) + labs(size="Significance") - } - if (size_by == "genesets") { + } else if (size_by == "genesets" ) { p <- p + scale_size_continuous(trans=scales::log10_trans()) + labs(size="Genesets\nSize") + } else if (size_by == "overlap" ) { + p <- p + scale_size_continuous(trans=scales::log10_trans()) + labs(size="Overlap\nSize") + } else { + stop("unrecognized 'size_by':", size_by) } - return(p) } From 66c2d2fa93f7741f50b18d9ceddbc4e1c78e22dd Mon Sep 17 00:00:00 2001 From: tetomonti Date: Fri, 20 Oct 2023 11:42:37 -0400 Subject: [PATCH 14/16] hits list modified to have space-comma-space as separator (it is now simply comma, which is often ambiguous) --- R/hyper_enrichment.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/hyper_enrichment.R b/R/hyper_enrichment.R index 87fcfce..cc33cc0 100644 --- a/R/hyper_enrichment.R +++ b/R/hyper_enrichment.R @@ -42,7 +42,8 @@ geneset=n.genesets, overlap=n.hits, background=background, - hits=sapply(genesets, function(x, y) paste(intersect(x, y), collapse=','), signature.found), + #hits=sapply(genesets, function(x, y) paste(intersect(x, y), collapse=','), signature.found), + hits=sapply(genesets, function(x, y) paste(intersect(x, y), collapse=' , '), signature.found), stringsAsFactors=FALSE) # Handle plots From f9a1b16ee61286f7e440ad02b2669dccc8509a85 Mon Sep 17 00:00:00 2001 From: Andrew Chen Date: Fri, 20 Oct 2023 18:07:53 -0400 Subject: [PATCH 15/16] Update Version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0697d53..6a42cc2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.99.0 +Version: 1.99.1 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Andrew", family="Chen", email="andrewdr@bu.edu", From ef8f2ec080688219ee15f23d8faad62214aa40a7 Mon Sep 17 00:00:00 2001 From: anfederico Date: Wed, 25 Oct 2023 22:49:07 -0400 Subject: [PATCH 16/16] Bump --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6a42cc2..744a069 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hypeR Title: An R Package For Geneset Enrichment Workflows -Version: 1.99.1 +Version: 2.0.0 Authors@R: c(person(given="Anthony", family="Federico", email="anfed@bu.edu", role=c("aut", "cre")), person(given="Andrew", family="Chen", email="andrewdr@bu.edu",