From e80fa05c41c066fcdc4d35f422a75a726ee23a1e Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 30 Apr 2024 11:42:35 -0400 Subject: [PATCH 1/6] bump x.y.z version to even y prior to creation of RELEASE_3_19 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d677dc0..ffe4b5d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: EpiCompare Title: Comparison, Benchmarking & QC of Epigenomic Datasets -Version: 1.7.5 +Version: 1.8.0 Authors@R: c( person(given = "Sera", family = "Choi", email = "serachoi1230@gmail.com", From e29605b2ea93b1b94d37e06bd43a6fc54855b76c Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 30 Apr 2024 11:42:35 -0400 Subject: [PATCH 2/6] bump x.y.z version to odd y following creation of RELEASE_3_19 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ffe4b5d..cb81b9d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: EpiCompare Title: Comparison, Benchmarking & QC of Epigenomic Datasets -Version: 1.8.0 +Version: 1.9.0 Authors@R: c( person(given = "Sera", family = "Choi", email = "serachoi1230@gmail.com", From 0d8732b4709b4abf8f262d756d55c5f2ce420b55 Mon Sep 17 00:00:00 2001 From: Tomrrr1 <76951517+Tomrrr1@users.noreply.github.com> Date: Mon, 8 Jul 2024 10:13:02 +0100 Subject: [PATCH 3/6] Edit author order. --- DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cb81b9d..e527c49 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: EpiCompare Title: Comparison, Benchmarking & QC of Epigenomic Datasets -Version: 1.9.0 +Version: 1.9.1 Authors@R: c( person(given = "Sera", family = "Choi", email = "serachoi1230@gmail.com", @@ -18,13 +18,13 @@ Authors@R: c( email = "alanmurph94@hotmail.com", role = "aut", comment = c(ORCID = "0000-0002-2487-8753")), + person(given="Thomas", family="Roberts", + email = "tomroberts.work15@gmail.com", + role = "cre") person(given="Nathan", family="Skene", email = "nathan.skene@gmail.com", role = "aut", comment = c(ORCID = "0000-0002-6807-3180")), - person(given="Thomas", family="Roberts", - email = "tomroberts.work15@gmail.com", - role = "cre") ) Description: EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. From a177857133082e957d85c0828222b23920b81c3d Mon Sep 17 00:00:00 2001 From: Tomrrr1 <76951517+Tomrrr1@users.noreply.github.com> Date: Tue, 9 Jul 2024 10:13:59 +0100 Subject: [PATCH 4/6] Edit DESCRIPTION and update plot_chromHMM.R --- .gitignore | 2 ++ DESCRIPTION | 10 +++++----- R/plot_chromHMM.R | 2 +- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 92553bd..f6a2d2f 100644 --- a/.gitignore +++ b/.gitignore @@ -57,3 +57,5 @@ vignettes/*.R *.knit.md # Ignore example html report for now inst/report +/doc/ +/Meta/ diff --git a/DESCRIPTION b/DESCRIPTION index cb81b9d..177b983 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: EpiCompare Title: Comparison, Benchmarking & QC of Epigenomic Datasets -Version: 1.9.0 +Version: 1.9.2 Authors@R: c( person(given = "Sera", family = "Choi", email = "serachoi1230@gmail.com", @@ -18,13 +18,13 @@ Authors@R: c( email = "alanmurph94@hotmail.com", role = "aut", comment = c(ORCID = "0000-0002-2487-8753")), + person(given="Thomas", family="Roberts", + email = "tomroberts.work15@gmail.com", + role = "cre"), person(given="Nathan", family="Skene", email = "nathan.skene@gmail.com", role = "aut", - comment = c(ORCID = "0000-0002-6807-3180")), - person(given="Thomas", family="Roberts", - email = "tomroberts.work15@gmail.com", - role = "cre") + comment = c(ORCID = "0000-0002-6807-3180")) ) Description: EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. diff --git a/R/plot_chromHMM.R b/R/plot_chromHMM.R index 7672d56..dd7c4b0 100644 --- a/R/plot_chromHMM.R +++ b/R/plot_chromHMM.R @@ -102,7 +102,7 @@ plot_chromHMM <- function(peaklist, fill = value)) + ggplot2::ylab("") + ggplot2::xlab("") + - ggplot2::scale_fill_viridis_c() + + ggplot2::scale_fill_viridis_b() + ggplot2::theme_minimal() + ggplot2::theme(axis.text = ggplot2::element_text(size = 11)) + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 315, From ec712243f3ed0c744b5b650cde81e8516bc46b06 Mon Sep 17 00:00:00 2001 From: Tomrrr1 <76951517+Tomrrr1@users.noreply.github.com> Date: Fri, 26 Jul 2024 11:33:47 +0100 Subject: [PATCH 5/6] Force version of downloadthis --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 177b983..c07d318 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: EpiCompare Title: Comparison, Benchmarking & QC of Epigenomic Datasets -Version: 1.9.2 +Version: 1.9.3 Authors@R: c( person(given = "Sera", family = "Choi", email = "serachoi1230@gmail.com", @@ -62,7 +62,7 @@ Imports: stringr, utils, BiocGenerics, - downloadthis, + downloadthis (<= 0.3.3), parallel Suggests: rworkflows, From d282d3e4320f59c70fdb765eb2048a1f7cd73313 Mon Sep 17 00:00:00 2001 From: Tomrrr1 <76951517+Tomrrr1@users.noreply.github.com> Date: Wed, 31 Jul 2024 19:52:39 +0100 Subject: [PATCH 6/6] Use latest version of downloadthis. --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index c07d318..135256f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -62,7 +62,7 @@ Imports: stringr, utils, BiocGenerics, - downloadthis (<= 0.3.3), + downloadthis, parallel Suggests: rworkflows,