From b9db7766042c20a8bdeb228fe5054a92599dcc66 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Mon, 29 Jun 2026 17:35:55 -0400 Subject: [PATCH 01/14] Update count_type to list with raw, clean, filt, norm options (default: filt) --- .codeocean/app-panel.json | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index fe13c29..a880123 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -53,9 +53,15 @@ "name": "Count type", "param_name": "count_type", "description": "Type of counts to use (e.g., filt, norm)", - "type": "text", - "value_type": "string", - "default_value": "filt" + "type": "list", + "value_type": "string", + "default_value": "filt", + "extra_data": [ + "raw", + "clean", + "filt", + "norm" + ] }, { "id": "sub_count_type_id", From 39db74540bfc19e731541979f2784677aaf4b82f Mon Sep 17 00:00:00 2001 From: phoman14 Date: Mon, 29 Jun 2026 18:00:49 -0400 Subject: [PATCH 02/14] Move count_type to first position in Basic category --- .codeocean/app-panel.json | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index a880123..9637eb9 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -16,40 +16,40 @@ "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 clustering and ordering options", - "icon": "📂" + "icon": "\ud83d\udcc2" }, { "id": "AdvGeneDisplay", "name": "Visualization", "description": "Visualization and plotting options", - "icon": "📊" + "icon": "\ud83d\udcca" }, { "id": "AdvSampleDisplay", "name": "Sample Display", - "icon": "📂" + "icon": "\ud83d\udcc2" }, { "id": "AdvHeatmapStyle", "name": "Heatmap Styling", - "icon": "📂" + "icon": "\ud83d\udcc2" } ], "parameters": [ { "id": "count_type_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "EzTg1ivlFDHEy9PI", "name": "Count type", "param_name": "count_type", "description": "Type of counts to use (e.g., filt, norm)", @@ -472,4 +472,4 @@ "file_name": "figures/heatmap/expr_heatmap.png" } ] -} \ No newline at end of file +} From f035b1c7fc2d72d7cf8c88521b5a708935726c38 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 02:38:43 -0400 Subject: [PATCH 03/14] Update heatmap panel controls --- .codeocean/app-panel.json | 124 ++++++++++++++++++++++++++++---------- 1 file changed, 92 insertions(+), 32 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index 9637eb9..c41907d 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -20,7 +20,7 @@ }, { "id": "EzTg1ivlFDHEy9PI", - "name": "Basic", + "name": "Gene Selection", "icon": "\ud83d\udcc2" }, { @@ -49,7 +49,7 @@ "parameters": [ { "id": "count_type_id", - "category": "EzTg1ivlFDHEy9PI", + "category": "7Rr6IxOMDucKMImp", "name": "Count type", "param_name": "count_type", "description": "Type of counts to use (e.g., filt, norm)", @@ -124,9 +124,13 @@ "name": "Include all genes", "param_name": "include_all_genes", "description": "Include all genes in heatmap", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "filter_top_genes_id", @@ -134,9 +138,13 @@ "name": "Filter top genes by variance", "param_name": "filter_top_genes_by_variance", "description": "Filter genes by variance", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "TRUE" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "top_genes_count_id", @@ -164,9 +172,13 @@ "name": "Cluster genes", "param_name": "cluster_genes", "description": "Cluster genes in heatmap", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "TRUE" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "gene_distance_metric_id", @@ -194,9 +206,13 @@ "name": "Center and rescale expression", "param_name": "center_and_rescale_expression", "description": "Center and rescale expression values", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "TRUE" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "cluster_samples_id", @@ -204,9 +220,13 @@ "name": "Cluster samples", "param_name": "cluster_samples", "description": "Cluster samples in heatmap", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "arrange_sample_cols_id", @@ -214,9 +234,13 @@ "name": "Arrange sample columns", "param_name": "arrange_sample_columns", "description": "Arrange sample columns", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "TRUE" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "order_by_gene_expr_id", @@ -224,9 +248,13 @@ "name": "Order by gene expression", "param_name": "order_by_gene_expression", "description": "Order samples by gene expression", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "gene_order_cols_id", @@ -274,9 +302,13 @@ "name": "Reorder dendrogram", "param_name": "reorder_dendrogram", "description": "Reorder dendrogram", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "reorder_dendrogram_order_id", @@ -293,9 +325,13 @@ "name": "Display gene dendrograms", "param_name": "display_gene_dendrograms", "description": "Display dendrograms for gene clustering", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "TRUE" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "display_gene_names_id", @@ -303,9 +339,13 @@ "name": "Display gene names", "param_name": "display_gene_names", "description": "Display gene names in heatmap", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "gene_name_font_size_id", @@ -323,9 +363,13 @@ "name": "Display sample dendrograms", "param_name": "display_smpl_dendrograms", "description": "Display dendrograms for sample clustering", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "TRUE" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "display_smpl_names_id", @@ -333,9 +377,13 @@ "name": "Display sample names", "param_name": "display_sample_names", "description": "Display sample names in heatmap", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "TRUE" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "sample_name_font_size_id", @@ -363,9 +411,13 @@ "name": "Assign group colors", "param_name": "assign_group_colors", "description": "Assign colors to sample groups", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "assign_color_sample_groups_id", @@ -412,9 +464,13 @@ "name": "Autoscale heatmap color", "param_name": "autoscale_heatmap_color", "description": "Automatically scale heatmap colors", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "TRUE" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "set_min_heatmap_color_id", @@ -462,9 +518,13 @@ "name": "Display numbers", "param_name": "display_numbers", "description": "Display numbers in heatmap cells", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] } ], "results": [ From 9a2d4f473378d029be9d65347683b8acf395a292 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 02:41:37 -0400 Subject: [PATCH 04/14] Rename heatmap basic input category --- .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 c41907d..000d91e 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -14,7 +14,7 @@ "categories": [ { "id": "7Rr6IxOMDucKMImp", - "name": "Input Data Parameters", + "name": "Basic Category", "description": "Options for defining input data", "icon": "\ud83d\udcc1" }, From 767944d59cd1c17ff89618dace080d1acaad4921 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 03:00:57 -0400 Subject: [PATCH 05/14] Add heatmap gene clustering options --- .codeocean/app-panel.json | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index 000d91e..deee555 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -186,9 +186,15 @@ "name": "Gene distance metric", "param_name": "gene_distance_metric", "description": "Distance metric for gene clustering", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "correlation" + "default_value": "correlation", + "extra_data": [ + "correlation", + "euclidean", + "maximum", + "manhattan" + ] }, { "id": "gene_clustering_method_id", @@ -196,9 +202,19 @@ "name": "Gene clustering method", "param_name": "gene_clustering_method", "description": "Clustering method for genes", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "average" + "default_value": "average", + "extra_data": [ + "average", + "complete", + "single", + "mcquitty", + "ward.D", + "ward.D2", + "centroid", + "median" + ] }, { "id": "center_rescale_id", From c094e4afa0d8902b573d2642431cec8519788d76 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 03:07:06 -0400 Subject: [PATCH 06/14] Split heatmap ordering categories --- .codeocean/app-panel.json | 72 ++++++++++++++++++++++++++++----------- 1 file changed, 52 insertions(+), 20 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index deee555..c7f133f 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -26,9 +26,21 @@ { "id": "FvI4Z2eb9sjL47Jt", "name": "Advanced", - "description": "Advanced clustering and ordering options", + "description": "Advanced parameters", "icon": "\ud83d\udcc2" }, + { + "id": "GeneOrder", + "name": "Gene Order", + "description": "Gene clustering and row ordering options", + "icon": "\ud83d\udcca" + }, + { + "id": "SampleOrder", + "name": "Sample Order", + "description": "Sample clustering and column ordering options", + "icon": "\ud83d\udcca" + }, { "id": "AdvGeneDisplay", "name": "Visualization", @@ -168,7 +180,7 @@ }, { "id": "cluster_genes_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "GeneOrder", "name": "Cluster genes", "param_name": "cluster_genes", "description": "Cluster genes in heatmap", @@ -182,7 +194,7 @@ }, { "id": "gene_distance_metric_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "GeneOrder", "name": "Gene distance metric", "param_name": "gene_distance_metric", "description": "Distance metric for gene clustering", @@ -198,7 +210,7 @@ }, { "id": "gene_clustering_method_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "GeneOrder", "name": "Gene clustering method", "param_name": "gene_clustering_method", "description": "Clustering method for genes", @@ -218,7 +230,7 @@ }, { "id": "center_rescale_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "GeneOrder", "name": "Center and rescale expression", "param_name": "center_and_rescale_expression", "description": "Center and rescale expression values", @@ -232,7 +244,7 @@ }, { "id": "cluster_samples_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Cluster samples", "param_name": "cluster_samples", "description": "Cluster samples in heatmap", @@ -246,7 +258,7 @@ }, { "id": "arrange_sample_cols_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Arrange sample columns", "param_name": "arrange_sample_columns", "description": "Arrange sample columns", @@ -260,7 +272,7 @@ }, { "id": "order_by_gene_expr_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Order by gene expression", "param_name": "order_by_gene_expression", "description": "Order samples by gene expression", @@ -274,7 +286,7 @@ }, { "id": "gene_order_cols_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Gene to order columns", "param_name": "gene_to_order_columns", "description": "Gene to use for ordering columns", @@ -284,37 +296,57 @@ }, { "id": "gene_expr_order_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Gene expression order", "param_name": "gene_expression_order", "description": "Order expression values (low_to_high or high_to_low)", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "low_to_high" + "default_value": "low_to_high", + "extra_data": [ + "low_to_high", + "high_to_low" + ] }, { "id": "smpl_distance_metric_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Sample distance metric", "param_name": "smpl_distance_metric", "description": "Distance metric for sample clustering", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "correlation" + "default_value": "correlation", + "extra_data": [ + "correlation", + "euclidean", + "maximum", + "manhattan" + ] }, { "id": "smpl_clustering_method_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Sample clustering method", "param_name": "smpl_clustering_method", "description": "Clustering method for samples", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "average" + "default_value": "average", + "extra_data": [ + "average", + "complete", + "single", + "mcquitty", + "ward.D", + "ward.D2", + "centroid", + "median" + ] }, { "id": "reorder_dendrogram_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Reorder dendrogram", "param_name": "reorder_dendrogram", "description": "Reorder dendrogram", @@ -328,7 +360,7 @@ }, { "id": "reorder_dendrogram_order_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Reorder dendrogram order", "param_name": "reorder_dendrogram_order", "description": "Order for reordering dendrogram", From 66f0a8e4e0b755cbfe7eb825e8bc348910fb7fea Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 03:14:18 -0400 Subject: [PATCH 07/14] Refine heatmap display categories --- .codeocean/app-panel.json | 122 +++++++++++++++++++------------------- 1 file changed, 61 insertions(+), 61 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index c7f133f..9c92833 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -36,15 +36,15 @@ "icon": "\ud83d\udcca" }, { - "id": "SampleOrder", - "name": "Sample Order", - "description": "Sample clustering and column ordering options", + "id": "GeneDisplay", + "name": "Gene Display", + "description": "Gene label and dendrogram display options", "icon": "\ud83d\udcca" }, { - "id": "AdvGeneDisplay", - "name": "Visualization", - "description": "Visualization and plotting options", + "id": "SampleOrder", + "name": "Sample Order", + "description": "Sample clustering and column ordering options", "icon": "\ud83d\udcca" }, { @@ -256,58 +256,6 @@ "FALSE" ] }, - { - "id": "arrange_sample_cols_id", - "category": "SampleOrder", - "name": "Arrange sample columns", - "param_name": "arrange_sample_columns", - "description": "Arrange sample columns", - "type": "list", - "value_type": "string", - "default_value": "TRUE", - "extra_data": [ - "TRUE", - "FALSE" - ] - }, - { - "id": "order_by_gene_expr_id", - "category": "SampleOrder", - "name": "Order by gene expression", - "param_name": "order_by_gene_expression", - "description": "Order samples by gene expression", - "type": "list", - "value_type": "string", - "default_value": "FALSE", - "extra_data": [ - "TRUE", - "FALSE" - ] - }, - { - "id": "gene_order_cols_id", - "category": "SampleOrder", - "name": "Gene to order columns", - "param_name": "gene_to_order_columns", - "description": "Gene to use for ordering columns", - "type": "text", - "value_type": "string", - "default_value": " " - }, - { - "id": "gene_expr_order_id", - "category": "SampleOrder", - "name": "Gene expression order", - "param_name": "gene_expression_order", - "description": "Order expression values (low_to_high or high_to_low)", - "type": "list", - "value_type": "string", - "default_value": "low_to_high", - "extra_data": [ - "low_to_high", - "high_to_low" - ] - }, { "id": "smpl_distance_metric_id", "category": "SampleOrder", @@ -367,9 +315,61 @@ "type": "text", "value_type": "string" }, + { + "id": "arrange_sample_cols_id", + "category": "SampleOrder", + "name": "Arrange sample columns", + "param_name": "arrange_sample_columns", + "description": "Arrange sample columns", + "type": "list", + "value_type": "string", + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] + }, + { + "id": "order_by_gene_expr_id", + "category": "SampleOrder", + "name": "Order by gene expression", + "param_name": "order_by_gene_expression", + "description": "Order samples by gene expression", + "type": "list", + "value_type": "string", + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] + }, + { + "id": "gene_order_cols_id", + "category": "SampleOrder", + "name": "Gene to order columns", + "param_name": "gene_to_order_columns", + "description": "Gene to use for ordering columns", + "type": "text", + "value_type": "string", + "default_value": " " + }, + { + "id": "gene_expr_order_id", + "category": "SampleOrder", + "name": "Gene expression order", + "param_name": "gene_expression_order", + "description": "Order expression values (low_to_high or high_to_low)", + "type": "list", + "value_type": "string", + "default_value": "low_to_high", + "extra_data": [ + "low_to_high", + "high_to_low" + ] + }, { "id": "display_gene_dendrograms_id", - "category": "AdvGeneDisplay", + "category": "GeneDisplay", "name": "Display gene dendrograms", "param_name": "display_gene_dendrograms", "description": "Display dendrograms for gene clustering", @@ -383,7 +383,7 @@ }, { "id": "display_gene_names_id", - "category": "AdvGeneDisplay", + "category": "GeneDisplay", "name": "Display gene names", "param_name": "display_gene_names", "description": "Display gene names in heatmap", @@ -397,7 +397,7 @@ }, { "id": "gene_name_font_size_id", - "category": "AdvGeneDisplay", + "category": "GeneDisplay", "name": "Gene name font size", "param_name": "gene_name_font_size", "description": "Font size for gene names", From 07e73a717445c555e83645a1d25368e4c916915a Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 03:19:49 -0400 Subject: [PATCH 08/14] Finalize heatmap category layout --- .codeocean/app-panel.json | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index 9c92833..a1659e2 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -23,12 +23,6 @@ "name": "Gene Selection", "icon": "\ud83d\udcc2" }, - { - "id": "FvI4Z2eb9sjL47Jt", - "name": "Advanced", - "description": "Advanced parameters", - "icon": "\ud83d\udcc2" - }, { "id": "GeneOrder", "name": "Gene Order", @@ -50,11 +44,17 @@ { "id": "AdvSampleDisplay", "name": "Sample Display", - "icon": "\ud83d\udcc2" + "icon": "\ud83d\udcca" }, { "id": "AdvHeatmapStyle", - "name": "Heatmap Styling", + "name": "Visualization Category", + "icon": "\ud83d\udcc2" + }, + { + "id": "FvI4Z2eb9sjL47Jt", + "name": "Advanced", + "description": "Advanced parameters", "icon": "\ud83d\udcc2" } ], From e101a1a666293db3b0896522759aae9a8649a4a9 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 03:21:57 -0400 Subject: [PATCH 09/14] Rename heatmap categories --- .codeocean/app-panel.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index a1659e2..136cec5 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -14,7 +14,7 @@ "categories": [ { "id": "7Rr6IxOMDucKMImp", - "name": "Basic Category", + "name": "Basic", "description": "Options for defining input data", "icon": "\ud83d\udcc1" }, @@ -48,7 +48,7 @@ }, { "id": "AdvHeatmapStyle", - "name": "Visualization Category", + "name": "Visualizations", "icon": "\ud83d\udcc2" }, { From dc6240504b46c828e77ef37444a9e3dc2116729f Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 03:27:21 -0400 Subject: [PATCH 10/14] Clarify heatmap scaling descriptions --- .codeocean/app-panel.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index 136cec5..f86bd52 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -233,7 +233,7 @@ "category": "GeneOrder", "name": "Center and rescale expression", "param_name": "center_and_rescale_expression", - "description": "Center and rescale expression values", + "description": "Transform the expression data before plotting by centering and scaling each gene across included samples. This affects clustering, ordering, and heatmap values.", "type": "list", "value_type": "string", "default_value": "TRUE", @@ -511,7 +511,7 @@ "category": "AdvHeatmapStyle", "name": "Autoscale heatmap color", "param_name": "autoscale_heatmap_color", - "description": "Automatically scale heatmap colors", + "description": "Automatically set the heatmap color range from the plotted data minimum and maximum. This changes only color mapping, not the expression data.", "type": "list", "value_type": "string", "default_value": "TRUE", From 2e7ed2a53bb88a243154cfeee764fe7c92f49061 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 03:28:17 -0400 Subject: [PATCH 11/14] Rename heatmap display category --- .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 f86bd52..e65a33f 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -48,7 +48,7 @@ }, { "id": "AdvHeatmapStyle", - "name": "Visualizations", + "name": "Heatmap Display", "icon": "\ud83d\udcc2" }, { From 4c840cf824937046f48e22a9f6ffe9bcef69c273 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 03:29:30 -0400 Subject: [PATCH 12/14] Update heatmap display icon --- .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 e65a33f..d575d1d 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -49,7 +49,7 @@ { "id": "AdvHeatmapStyle", "name": "Heatmap Display", - "icon": "\ud83d\udcc2" + "icon": "\ud83d\udcca" }, { "id": "FvI4Z2eb9sjL47Jt", From f2d3b7bd47415d1e63c903a01399b6f9093fdd43 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 13:40:42 -0400 Subject: [PATCH 13/14] Update changelog for parameter UI changes --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 54cae12..16b253a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ ## development version +- Improved the Code Ocean parameter UI for the plot expr heatmap capsule (#4). ## v3.0 - The MOSuite package is now available in `code/MOSuite`. (#2) @@ -17,4 +18,4 @@ Initial release - `1d64179` \ No newline at end of file + `1d64179` From 0a7024f5672a6b74b9808b476c0ac459ec07af57 Mon Sep 17 00:00:00 2001 From: phoman14 Date: Tue, 30 Jun 2026 14:10:59 -0400 Subject: [PATCH 14/14] 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 16b253a..29a5be6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,7 @@ ## development version -- Improved the Code Ocean parameter UI for the plot expr heatmap capsule (#4). +- Improved the Code Ocean parameter UI for the plot expr heatmap capsule (#4, @phoman14). ## v3.0 - The MOSuite package is now available in `code/MOSuite`. (#2)