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kelly-sovacool merged 11 commits into from
Aug 3, 2026
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docs(panel): sync parameter descriptions #7

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88c5d21
Require count type selection
phoman14 Jul 16, 2026
e838012
Update count type app-panel options
phoman14 Jul 17, 2026
8943b49
chore(syncweaver): update MOSuite source to main
phoman14 Jul 31, 2026
148ca4b
docs(panel): sync parameter descriptions
phoman14 Jul 31, 2026
b7eaff1
docs(changelog): add PR entry
phoman14 Jul 31, 2026
8b84c3f
Merge remote-tracking branch 'origin/main' into dev-homan
phoman14 Jul 31, 2026
dbfe8d4
test: add syncweaver lock coverage
phoman14 Jul 31, 2026
a9ee7f7
test: remove syncweaver lock tests
phoman14 Aug 3, 2026
985e779
Update CHANGELOG.md
phoman14 Aug 3, 2026
54754bb
chore: Merge branch 'main' into dev-homan
kelly-sovacool Aug 3, 2026
bf846fc
Merge branch 'main' into dev-homan
kelly-sovacool Aug 3, 2026
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86 changes: 44 additions & 42 deletions .codeocean/app-panel.json
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Original file line number Diff line number Diff line change
Expand Up @@ -64,23 +64,25 @@
"category": "7Rr6IxOMDucKMImp",
"name": "Count type",
"param_name": "count_type",
"description": "Type of counts to use (e.g., filt, norm)",
"description": "The type of counts to use. This must be a name in the counts slot, moo@counts.",
"type": "list",
"value_type": "string",
"default_value": "filt",
"default_value": null,
"required": true,
"extra_data": [
"raw",
"clean",
"filt",
"norm"
"norm",
"batch"
]
},
{
"id": "sub_count_type_id",
"category": "FvI4Z2eb9sjL47Jt",
"name": "Sub count type",
"param_name": "sub_count_type",
"description": "Sub count type if count_type is a list",
"description": "Used if count_type is a list in the counts slot. This must be a name in moo@counts[[count_type]].",
"type": "text",
"value_type": "string"
},
Expand All @@ -89,7 +91,7 @@
"category": "FvI4Z2eb9sjL47Jt",
"name": "Sample ID column name",
"param_name": "sample_id_colname",
"description": "Column name for sample IDs",
"description": "The column from the sample metadata containing the sample names. The names in this column must exactly match the names used as sample column names in the input counts matrix.",
"type": "text",
"value_type": "string"
},
Expand All @@ -98,7 +100,7 @@
"category": "FvI4Z2eb9sjL47Jt",
"name": "Feature ID column name",
"param_name": "feature_id_colname",
"description": "Column name for feature IDs",
"description": "The column from the counts data containing the Feature IDs, usually Gene or Protein ID. This is usually the first column of the input counts matrix. Only columns of text type from the input counts matrix are available to select for this parameter.",
"type": "text",
"value_type": "string"
},
Expand All @@ -107,7 +109,7 @@
"category": "7Rr6IxOMDucKMImp",
"name": "Group column name",
"param_name": "group_colname",
"description": "Column name for sample groups",
"description": "The column from the sample metadata containing the sample group information. This is usually a column showing to which experimental treatments each sample belongs, such as WildType, Knockout, Tumor, Normal, Before, or After.",
"type": "text",
"value_type": "string",
"default_value": "Group"
Expand All @@ -117,7 +119,7 @@
"category": "7Rr6IxOMDucKMImp",
"name": "Label column name",
"param_name": "label_colname",
"description": "Column name for sample labels",
"description": "The column from the sample metadata containing the sample labels as you wish them to appear in plots. This can be the same Sample Names Column. You may select a different column with shorter labels for display on figures. The selected column should contain unique names for each sample.",
"type": "text",
"value_type": "string"
},
Expand All @@ -126,7 +128,7 @@
"category": "7Rr6IxOMDucKMImp",
"name": "Samples to include",
"param_name": "samples_to_include",
"description": "Comma-separated list of samples to include",
"description": "Which samples would you like to include? Usually, you will choose all sample columns, or you could choose to remove certain samples. Samples excluded here will be removed in this step and from downstream analysis.",
"type": "text",
"value_type": "string"
},
Expand All @@ -135,7 +137,7 @@
"category": "EzTg1ivlFDHEy9PI",
"name": "Include all genes",
"param_name": "include_all_genes",
"description": "Include all genes in heatmap",
"description": "Set to TRUE if all genes are to be included. Set to FALSE if you want to filter genes by variance or provide a list of specific genes for the heatmap.",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
Expand All @@ -149,7 +151,7 @@
"category": "EzTg1ivlFDHEy9PI",
"name": "Filter top genes by variance",
"param_name": "filter_top_genes_by_variance",
"description": "Filter genes by variance",
"description": "Set to TRUE to include only the top genes by variance. Set to FALSE if you do not want to filter genes by variance.",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
Expand All @@ -163,7 +165,7 @@
"category": "EzTg1ivlFDHEy9PI",
"name": "Top genes by variance",
"param_name": "top_genes_by_variance_to_include",
"description": "Number of top genes by variance to include",
"description": "The number of genes to include if filtering genes by variance. This parameter is ignored if Filter top genes by variance is set to FALSE.",
"type": "text",
"value_type": "string",
"default_value": "500"
Expand All @@ -173,7 +175,7 @@
"category": "EzTg1ivlFDHEy9PI",
"name": "Specific genes to include",
"param_name": "specific_genes_to_include_in_heatmap",
"description": "Comma-separated list of specific genes",
"description": "Enter the gene symbols to include in the heatmap, with each gene symbol separated from the others. You can also paste in a column of gene names from a spreadsheet. This parameter is ignored if Include all genes is set to TRUE.",
"type": "text",
"value_type": "string",
"default_value": "None"
Expand All @@ -183,7 +185,7 @@
"category": "GeneOrder",
"name": "Cluster genes",
"param_name": "cluster_genes",
"description": "Cluster genes in heatmap",
"description": "Choose whether to cluster the rows, which represent genes. If TRUE, rows will have clustering applied. If FALSE, clustering will not be applied to rows.",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
Expand All @@ -197,7 +199,7 @@
"category": "GeneOrder",
"name": "Gene distance metric",
"param_name": "gene_distance_metric",
"description": "Distance metric for gene clustering",
"description": "Distance metric to be used in clustering genes.",
"type": "list",
"value_type": "string",
"default_value": "correlation",
Expand All @@ -213,7 +215,7 @@
"category": "GeneOrder",
"name": "Gene clustering method",
"param_name": "gene_clustering_method",
"description": "Clustering method for genes",
"description": "Clustering method to be used in clustering genes.",
"type": "list",
"value_type": "string",
"default_value": "average",
Expand Down Expand Up @@ -247,7 +249,7 @@
"category": "SampleOrder",
"name": "Cluster samples",
"param_name": "cluster_samples",
"description": "Cluster samples in heatmap",
"description": "Choose whether to cluster the columns, which represent samples. If TRUE, columns will have clustering applied. If FALSE, clustering will not be applied to columns.",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
Expand All @@ -261,7 +263,7 @@
"category": "SampleOrder",
"name": "Sample distance metric",
"param_name": "smpl_distance_metric",
"description": "Distance metric for sample clustering",
"description": "Distance metric to be used in clustering samples.",
"type": "list",
"value_type": "string",
"default_value": "correlation",
Expand All @@ -277,7 +279,7 @@
"category": "SampleOrder",
"name": "Sample clustering method",
"param_name": "smpl_clustering_method",
"description": "Clustering method for samples",
"description": "Clustering method to be used in clustering samples.",
"type": "list",
"value_type": "string",
"default_value": "average",
Expand All @@ -297,7 +299,7 @@
"category": "SampleOrder",
"name": "Reorder dendrogram",
"param_name": "reorder_dendrogram",
"description": "Reorder dendrogram",
"description": "If TRUE, set the order of the sample dendrogram using Reorder dendrogram order.",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
Expand All @@ -311,7 +313,7 @@
"category": "SampleOrder",
"name": "Reorder dendrogram order",
"param_name": "reorder_dendrogram_order",
"description": "Order for reordering dendrogram",
"description": "Reorder the samples, which are columns, of the dendrogram by name.",
"type": "text",
"value_type": "string"
},
Expand All @@ -320,7 +322,7 @@
"category": "SampleOrder",
"name": "Arrange sample columns",
"param_name": "arrange_sample_columns",
"description": "Arrange sample columns",
"description": "If TRUE, arrange columns by annotation groups. If FALSE and Cluster samples is FALSE, samples appear in the input order.",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
Expand All @@ -334,7 +336,7 @@
"category": "SampleOrder",
"name": "Order by gene expression",
"param_name": "order_by_gene_expression",
"description": "Order samples by gene expression",
"description": "If TRUE, order samples by the selected gene expression values.",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
Expand All @@ -348,7 +350,7 @@
"category": "SampleOrder",
"name": "Gene to order columns",
"param_name": "gene_to_order_columns",
"description": "Gene to use for ordering columns",
"description": "Gene to use for ordering columns by expression levels.",
"type": "text",
"value_type": "string",
"default_value": " "
Expand All @@ -358,7 +360,7 @@
"category": "SampleOrder",
"name": "Gene expression order",
"param_name": "gene_expression_order",
"description": "Order expression values (low_to_high or high_to_low)",
"description": "Choose direction for gene expression ordering.",
"type": "list",
"value_type": "string",
"default_value": "low_to_high",
Expand All @@ -372,7 +374,7 @@
"category": "GeneDisplay",
"name": "Display gene dendrograms",
"param_name": "display_gene_dendrograms",
"description": "Display dendrograms for gene clustering",
"description": "Set to TRUE to show gene dendrograms. Set to FALSE to hide dendrograms.",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
Expand All @@ -386,7 +388,7 @@
"category": "GeneDisplay",
"name": "Display gene names",
"param_name": "display_gene_names",
"description": "Display gene names in heatmap",
"description": "Set to TRUE to display gene names on the right side of the heatmap. Set to FALSE to hide gene names.",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
Expand All @@ -400,7 +402,7 @@
"category": "GeneDisplay",
"name": "Gene name font size",
"param_name": "gene_name_font_size",
"description": "Font size for gene names",
"description": "Font size for gene names. Toggle Display gene names to FALSE to hide gene labels.",
"type": "text",
"value_type": "string",
"default_value": "4"
Expand All @@ -410,7 +412,7 @@
"category": "AdvSampleDisplay",
"name": "Display sample dendrograms",
"param_name": "display_smpl_dendrograms",
"description": "Display dendrograms for sample clustering",
"description": "Set to TRUE to show sample dendrograms. Set to FALSE to hide dendrograms.",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
Expand All @@ -424,7 +426,7 @@
"category": "AdvSampleDisplay",
"name": "Display sample names",
"param_name": "display_sample_names",
"description": "Display sample names in heatmap",
"description": "Set to TRUE to display sample names on the plot. Set to FALSE to hide sample names.",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
Expand All @@ -438,7 +440,7 @@
"category": "AdvSampleDisplay",
"name": "Sample name font size",
"param_name": "sample_name_font_size",
"description": "Font size for sample names",
"description": "Font size for sample names. Toggle Display sample names to FALSE to hide sample names.",
"type": "text",
"value_type": "string",
"default_value": "8"
Expand All @@ -448,7 +450,7 @@
"category": "AdvSampleDisplay",
"name": "Group columns",
"param_name": "group_columns",
"description": "Columns for grouping samples",
"description": "Columns containing the sample groups for annotation tracks.",
"type": "text",
"value_type": "string",
"default_value": "Group,Replicate,Batch"
Expand All @@ -458,7 +460,7 @@
"category": "AdvSampleDisplay",
"name": "Assign group colors",
"param_name": "assign_group_colors",
"description": "Assign colors to sample groups",
"description": "If TRUE, set the colors assigned to sample groups.",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
Expand All @@ -472,7 +474,7 @@
"category": "AdvSampleDisplay",
"name": "Assign color to sample groups",
"param_name": "assign_color_to_sample_groups",
"description": "Assignment of colors to sample groups",
"description": "Enter each sample group color assignment in the format group_name: color. This parameter is ignored if Assign group colors is set to FALSE.",
"type": "text",
"value_type": "string"
},
Expand All @@ -481,7 +483,7 @@
"category": "AdvHeatmapStyle",
"name": "Color values",
"param_name": "color_values",
"description": "Comma-separated color values for heatmap",
"description": "Vector of colors as hex values or names recognized by R. Unnamed colors are assigned by factor level order when the grouping column is a factor; otherwise, they are assigned in the order groups first appear in the metadata column.",
"type": "text",
"value_type": "string",
"default_value": "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500"
Expand All @@ -491,7 +493,7 @@
"category": "AdvHeatmapStyle",
"name": "Group colors",
"param_name": "group_colors",
"description": "Comma-separated colors for groups",
"description": "Colors for sample group annotations.",
"type": "text",
"value_type": "string",
"default_value": "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500"
Expand All @@ -501,7 +503,7 @@
"category": "AdvHeatmapStyle",
"name": "Heatmap color scheme",
"param_name": "heatmap_color_scheme",
"description": "Color scheme for heatmap",
"description": "Color scheme for the heatmap.",
"type": "text",
"value_type": "string",
"default_value": "Default"
Expand All @@ -525,7 +527,7 @@
"category": "AdvHeatmapStyle",
"name": "Minimum heatmap color value",
"param_name": "set_min_heatmap_color",
"description": "Minimum value for heatmap color scale",
"description": "If Autoscale heatmap color is set to FALSE, set the minimum heatmap z-score value.",
"type": "text",
"value_type": "string",
"default_value": "-2"
Expand All @@ -535,7 +537,7 @@
"category": "AdvHeatmapStyle",
"name": "Maximum heatmap color value",
"param_name": "set_max_heatmap_color",
"description": "Maximum value for heatmap color scale",
"description": "If Autoscale heatmap color is set to FALSE, set the maximum heatmap z-score value.",
"type": "text",
"value_type": "string",
"default_value": "2"
Expand All @@ -545,7 +547,7 @@
"category": "AdvHeatmapStyle",
"name": "Aspect ratio",
"param_name": "aspect_ratio",
"description": "Aspect ratio of heatmap",
"description": "Set the figure aspect ratio. Ratio refers to the entire figure including the legend.",
"type": "text",
"value_type": "string",
"default_value": "Auto"
Expand All @@ -555,7 +557,7 @@
"category": "AdvHeatmapStyle",
"name": "Legend font size",
"param_name": "legend_font_size",
"description": "Font size for legend",
"description": "Set font size for the figure legend.",
"type": "text",
"value_type": "string",
"default_value": "10"
Expand All @@ -565,7 +567,7 @@
"category": "AdvHeatmapStyle",
"name": "Display numbers",
"param_name": "display_numbers",
"description": "Display numbers in heatmap cells",
"description": "Set to TRUE to display numerical heat values in heatmap cells. Set to FALSE to hide these numbers.",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
Expand Down
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,7 @@

## development version

- Sync Code Ocean app panel parameter descriptions with MOSuite package documentation for MOSuite v0.4.1 (#7, @phoman14).
- Improved the Code Ocean parameter UI for the plot expr heatmap capsule (#4, @phoman14).
- Use MOSuite v0.3.2. (#1, @kelly-sovacool)

Expand Down
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