From 71854ab164949d26347ff9754a2460f655672086 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Mon, 29 Jun 2026 17:28:38 -0400 Subject: [PATCH 1/7] Update count_type to list with raw, clean, filt options (default: filt) --- .codeocean/app-panel.json | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index 5e79769..1c8f057 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -71,9 +71,14 @@ "name": "Count type", "param_name": "count_type", "description": "Counts slot name to use for differential expression (e.g., filt)", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "filt" + "default_value": "filt", + "extra_data": [ + "raw", + "clean", + "filt" + ] }, { "id": "WoZUI91NYysibcVj", From 6076e027bace02899f777461f5425928ff45bac8 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Mon, 29 Jun 2026 18:00:48 -0400 Subject: [PATCH 2/7] Move count_type to first position in Basic category --- .codeocean/app-panel.json | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index 1c8f057..cdab396 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -16,21 +16,36 @@ "id": "7Rr6IxOMDucKMImp", "name": "Input Data Parameters", "description": "Options for defining input data", - "icon": "📁" + "icon": "\ud83d\udcc1" }, { "id": "EzTg1ivlFDHEy9PI", "name": "Basic", - "icon": "📂" + "icon": "\ud83d\udcc2" }, { "id": "FvI4Z2eb9sjL47Jt", "name": "Advanced", "description": "Advanced parameters", - "icon": "📂" + "icon": "\ud83d\udcc2" } ], "parameters": [ + { + "id": "qsXhqvyKgDh3Vz8u", + "category": "EzTg1ivlFDHEy9PI", + "name": "Count type", + "param_name": "count_type", + "description": "Counts slot name to use for differential expression (e.g., filt)", + "type": "list", + "value_type": "string", + "default_value": "filt", + "extra_data": [ + "raw", + "clean", + "filt" + ] + }, { "id": "73xRrg0JvDvhEkPN", "category": "EzTg1ivlFDHEy9PI", @@ -65,21 +80,6 @@ "default_value": "Group,Batch", "required": true }, - { - "id": "qsXhqvyKgDh3Vz8u", - "category": "FvI4Z2eb9sjL47Jt", - "name": "Count type", - "param_name": "count_type", - "description": "Counts slot name to use for differential expression (e.g., filt)", - "type": "list", - "value_type": "string", - "default_value": "filt", - "extra_data": [ - "raw", - "clean", - "filt" - ] - }, { "id": "WoZUI91NYysibcVj", "category": "FvI4Z2eb9sjL47Jt", @@ -152,4 +152,4 @@ "file_name": "figures/diff/mean-variance.png" } ] -} \ No newline at end of file +} From 00cdcc0ca52087c84cb12d536317f10ef98a8b39 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 01:17:59 -0400 Subject: [PATCH 3/7] Use list controls for differential parameters --- .codeocean/app-panel.json | 32 +++++++++++++++++++++++++------- 1 file changed, 25 insertions(+), 7 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index cdab396..e071600 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -122,9 +122,13 @@ "name": "Input in log counts", "param_name": "input_in_log_counts", "description": "Set TRUE if counts are already log2-transformed", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "yxhLfINFuSTTS3Fj", @@ -132,19 +136,33 @@ "name": "Return mean and sd", "param_name": "return_mean_and_sd", "description": "Return group means and standard deviations in addition to DE estimates", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "Uq2LuAF8ff8pzM9e", "category": "FvI4Z2eb9sjL47Jt", "name": "voom normalization method", "param_name": "voom_normalization_method", - "description": "Normalization method passed to limma::voom", - "type": "text", + "description": "Normalization method for differential expression. edgeR methods are applied with calcNormFactors before voom; limma methods are passed to voom normalize.", + "type": "list", "value_type": "string", - "default_value": "quantile" + "default_value": "quantile", + "extra_data": [ + "TMM", + "TMMwzp", + "RLE", + "upperquartile", + "none", + "scale", + "quantile", + "cyclicloess" + ] } ], "results": [ From 4740ab0ec7b975c1fbfd89b49183803a1e231109 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 02:06:14 -0400 Subject: [PATCH 4/7] Order diff normalization options --- .codeocean/app-panel.json | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index e071600..26abedf 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -154,14 +154,14 @@ "value_type": "string", "default_value": "quantile", "extra_data": [ + "quantile", + "scale", + "cyclicloess", + "none", "TMM", "TMMwzp", "RLE", - "upperquartile", - "none", - "scale", - "quantile", - "cyclicloess" + "upperquartile" ] } ], From c4b87c263ae6451f95990077ce2c4a42cc100454 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 02:09:23 -0400 Subject: [PATCH 5/7] Clarify diff normalization methods --- .codeocean/app-panel.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index 26abedf..4d81488 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -149,7 +149,7 @@ "category": "FvI4Z2eb9sjL47Jt", "name": "voom normalization method", "param_name": "voom_normalization_method", - "description": "Normalization method for differential expression. edgeR methods are applied with calcNormFactors before voom; limma methods are passed to voom normalize.", + "description": "Normalization method for differential expression. edgeR methods are applied with calcNormFactors before voom; limma methods are passed to voom normalize. limma options: quantile, scale, cyclicloess, none. edgeR options: TMM, TMMwzp, RLE, upperquartile.", "type": "list", "value_type": "string", "default_value": "quantile", From 0a973786fa2ac2b971fdfe32e823167b82704994 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 13:40:29 -0400 Subject: [PATCH 6/7] Update changelog for parameter UI changes --- CHANGELOG.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c042385..7800096 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,9 @@ # Code Ocean capsule - MOSuite - differential expression analysis +## Development version + +- Improved the Code Ocean parameter UI for the diff counts capsule (#3). + ## v3.0 - The MOSuite package is now available in `code/MOSuite`. (#2) @@ -17,4 +21,4 @@ - Initial release. - Uses MOSuite v0.2.1-dev docker image. - `8f9bdf7` \ No newline at end of file + `8f9bdf7` From 959b86c706653547acd3387fdfb94cb7930bcf09 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 14:10:57 -0400 Subject: [PATCH 7/7] Add author handle to changelog entry --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7800096..75d9176 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,7 @@ ## Development version -- Improved the Code Ocean parameter UI for the diff counts capsule (#3). +- Improved the Code Ocean parameter UI for the diff counts capsule (#3, @phoman14). ## v3.0