diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index fe13c29..d575d1d 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -14,48 +14,66 @@ "categories": [ { "id": "7Rr6IxOMDucKMImp", - "name": "Input Data Parameters", + "name": "Basic", "description": "Options for defining input data", - "icon": "📁" + "icon": "\ud83d\udcc1" }, { "id": "EzTg1ivlFDHEy9PI", - "name": "Basic", - "icon": "📂" + "name": "Gene Selection", + "icon": "\ud83d\udcc2" }, { - "id": "FvI4Z2eb9sjL47Jt", - "name": "Advanced", - "description": "Advanced clustering and ordering options", - "icon": "📂" + "id": "GeneOrder", + "name": "Gene Order", + "description": "Gene clustering and row ordering options", + "icon": "\ud83d\udcca" }, { - "id": "AdvGeneDisplay", - "name": "Visualization", - "description": "Visualization and plotting options", - "icon": "📊" + "id": "GeneDisplay", + "name": "Gene Display", + "description": "Gene label and dendrogram display options", + "icon": "\ud83d\udcca" + }, + { + "id": "SampleOrder", + "name": "Sample Order", + "description": "Sample clustering and column ordering options", + "icon": "\ud83d\udcca" }, { "id": "AdvSampleDisplay", "name": "Sample Display", - "icon": "📂" + "icon": "\ud83d\udcca" }, { "id": "AdvHeatmapStyle", - "name": "Heatmap Styling", - "icon": "📂" + "name": "Heatmap Display", + "icon": "\ud83d\udcca" + }, + { + "id": "FvI4Z2eb9sjL47Jt", + "name": "Advanced", + "description": "Advanced parameters", + "icon": "\ud83d\udcc2" } ], "parameters": [ { "id": "count_type_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "7Rr6IxOMDucKMImp", "name": "Count type", "param_name": "count_type", "description": "Type of counts to use (e.g., filt, norm)", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "filt" + "default_value": "filt", + "extra_data": [ + "raw", + "clean", + "filt", + "norm" + ] }, { "id": "sub_count_type_id", @@ -118,9 +136,13 @@ "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", @@ -128,9 +150,13 @@ "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", @@ -154,77 +180,172 @@ }, { "id": "cluster_genes_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "GeneOrder", "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", - "category": "FvI4Z2eb9sjL47Jt", + "category": "GeneOrder", "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", - "category": "FvI4Z2eb9sjL47Jt", + "category": "GeneOrder", "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", - "category": "FvI4Z2eb9sjL47Jt", + "category": "GeneOrder", "name": "Center and rescale expression", "param_name": "center_and_rescale_expression", - "description": "Center and rescale expression values", - "type": "text", + "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" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "cluster_samples_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Cluster samples", "param_name": "cluster_samples", "description": "Cluster samples in heatmap", - "type": "text", + "type": "list", + "value_type": "string", + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] + }, + { + "id": "smpl_distance_metric_id", + "category": "SampleOrder", + "name": "Sample distance metric", + "param_name": "smpl_distance_metric", + "description": "Distance metric for sample clustering", + "type": "list", + "value_type": "string", + "default_value": "correlation", + "extra_data": [ + "correlation", + "euclidean", + "maximum", + "manhattan" + ] + }, + { + "id": "smpl_clustering_method_id", + "category": "SampleOrder", + "name": "Sample clustering method", + "param_name": "smpl_clustering_method", + "description": "Clustering method for samples", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "average", + "extra_data": [ + "average", + "complete", + "single", + "mcquitty", + "ward.D", + "ward.D2", + "centroid", + "median" + ] + }, + { + "id": "reorder_dendrogram_id", + "category": "SampleOrder", + "name": "Reorder dendrogram", + "param_name": "reorder_dendrogram", + "description": "Reorder dendrogram", + "type": "list", + "value_type": "string", + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] + }, + { + "id": "reorder_dendrogram_order_id", + "category": "SampleOrder", + "name": "Reorder dendrogram order", + "param_name": "reorder_dendrogram_order", + "description": "Order for reordering dendrogram", + "type": "text", + "value_type": "string" }, { "id": "arrange_sample_cols_id", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "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", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "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", - "category": "FvI4Z2eb9sjL47Jt", + "category": "SampleOrder", "name": "Gene to order columns", "param_name": "gene_to_order_columns", "description": "Gene to use for ordering columns", @@ -234,76 +355,49 @@ }, { "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", - "value_type": "string", - "default_value": "low_to_high" - }, - { - "id": "smpl_distance_metric_id", - "category": "FvI4Z2eb9sjL47Jt", - "name": "Sample distance metric", - "param_name": "smpl_distance_metric", - "description": "Distance metric for sample clustering", - "type": "text", - "value_type": "string", - "default_value": "correlation" - }, - { - "id": "smpl_clustering_method_id", - "category": "FvI4Z2eb9sjL47Jt", - "name": "Sample clustering method", - "param_name": "smpl_clustering_method", - "description": "Clustering method for samples", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "average" - }, - { - "id": "reorder_dendrogram_id", - "category": "FvI4Z2eb9sjL47Jt", - "name": "Reorder dendrogram", - "param_name": "reorder_dendrogram", - "description": "Reorder dendrogram", - "type": "text", - "value_type": "string", - "default_value": "FALSE" - }, - { - "id": "reorder_dendrogram_order_id", - "category": "FvI4Z2eb9sjL47Jt", - "name": "Reorder dendrogram order", - "param_name": "reorder_dendrogram_order", - "description": "Order for reordering dendrogram", - "type": "text", - "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", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "TRUE" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "display_gene_names_id", - "category": "AdvGeneDisplay", + "category": "GeneDisplay", "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", - "category": "AdvGeneDisplay", + "category": "GeneDisplay", "name": "Gene name font size", "param_name": "gene_name_font_size", "description": "Font size for gene names", @@ -317,9 +411,13 @@ "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", @@ -327,9 +425,13 @@ "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", @@ -357,9 +459,13 @@ "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", @@ -405,10 +511,14 @@ "category": "AdvHeatmapStyle", "name": "Autoscale heatmap color", "param_name": "autoscale_heatmap_color", - "description": "Automatically scale heatmap colors", - "type": "text", + "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" + "default_value": "TRUE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "set_min_heatmap_color_id", @@ -456,9 +566,13 @@ "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": [ @@ -466,4 +580,4 @@ "file_name": "figures/heatmap/expr_heatmap.png" } ] -} \ No newline at end of file +} diff --git a/CHANGELOG.md b/CHANGELOG.md index 54cae12..29a5be6 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, @phoman14). ## 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`