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kelly-sovacool merged 18 commits into from
Aug 3, 2026
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docs(panel): sync parameter descriptions #10

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cc5fecc
Order QC figure outputs
phoman14 Jul 16, 2026
9c504ac
Order QC outputs from main script
phoman14 Jul 16, 2026
ba72630
Restore capsule main script
phoman14 Jul 16, 2026
5b79b0c
Update PCA point size default
phoman14 Jul 17, 2026
34efd05
Update PCA label controls
phoman14 Jul 21, 2026
ca515aa
Update vendored MOSuite plotting defaults
phoman14 Jul 21, 2026
ebb6a88
Revert "Update vendored MOSuite plotting defaults"
phoman14 Jul 21, 2026
ab59655
Sync MOSuite subtree to FigOutSync
phoman14 Jul 21, 2026
68f7d22
test: add normalize plotting CLI coverage
phoman14 Jul 23, 2026
e666768
chore(syncweaver): update MOSuite source to main
phoman14 Jul 31, 2026
597886b
docs(panel): sync parameter descriptions
phoman14 Jul 31, 2026
9d79e04
docs(changelog): add PR entry
phoman14 Jul 31, 2026
bc4a8e4
chore(merge): merge main into dev-homan
phoman14 Jul 31, 2026
242fc44
test: add syncweaver lock coverage
phoman14 Jul 31, 2026
550153f
test: fix normalize counts CLI test paths
phoman14 Jul 31, 2026
9e5058f
test: remove syncweaver lock tests
phoman14 Aug 3, 2026
9fc9e5b
chore: Merge branch 'main' into dev-homan
kelly-sovacool Aug 3, 2026
29dd722
Update CHANGELOG.md
phoman14 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 @@ -60,7 +60,7 @@
"category": "gn9FXwemlVazWQIo",
"name": "Count type",
"param_name": "count_type",
"description": "Type of counts to normalize. Must be a count type in names(moo@counts)",
"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",
Expand All @@ -75,7 +75,7 @@
"category": "gn9FXwemlVazWQIo",
"name": "Normalization type",
"param_name": "norm_type",
"description": "Normalization type (default: voom)",
"description": "Normalization type. The voom option uses limma::voom.",
"type": "list",
"value_type": "string",
"default_value": "voom",
Expand All @@ -88,7 +88,7 @@
"category": "gn9FXwemlVazWQIo",
"name": "Group column name",
"param_name": "group_colname",
"description": "Column from sample metadata containing sample group information (e.g. treatment, phenotype)",
"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 @@ -98,7 +98,7 @@
"category": "gn9FXwemlVazWQIo",
"name": "Input already log2",
"param_name": "input_in_log_counts",
"description": "Set TRUE if counts are already log2-transformed",
"description": "Set this to TRUE if counts are already log2-transformed.",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
Expand All @@ -112,7 +112,7 @@
"category": "gn9FXwemlVazWQIo",
"name": "Voom normalization method",
"param_name": "voom_normalization_method",
"description": "Normalization method for limma::voom",
"description": "Normalization method to be applied to the logCPM values when using limma::voom.",
"type": "list",
"value_type": "string",
"default_value": "quantile",
Expand All @@ -128,8 +128,8 @@
"category": "XqgPq28Eo5VCFSZu",
"name": "Feature ID column name",
"param_name": "feature_id_colname",
"description": "Column from the counts data containing Feature IDs",
"help_text": "Leave blank to use the first column in the counts matrix by default",
"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.",
"help_text": "Leaving this empty uses the first column in the counts matrix.",
"type": "text",
"value_type": "string"
},
Expand All @@ -138,8 +138,8 @@
"category": "XqgPq28Eo5VCFSZu",
"name": "Sample ID column name",
"param_name": "sample_id_colname",
"description": "Column from the sample metadata containing sample names",
"help_text": "Leave blank to use the first column in the sample metadata by default",
"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.",
"help_text": "Leaving this empty uses the first column in the sample metadata.",
"type": "text",
"value_type": "string"
},
Expand All @@ -148,18 +148,19 @@
"category": "VisGeneral",
"name": "Label column name",
"param_name": "label_colname",
"description": "Column from sample metadata containing labels for plots",
"help_text": "Leave blank to use the sample ID column",
"description": "The column from the sample metadata containing the sample labels as you wish them to appear in heatmap and PCA figures. 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.",
"help_text": "Use Add labels to PCA to control whether these labels appear on PCA points.",
"type": "text",
"value_type": "string"
"value_type": "string",
"default_value": "Label"
},
{
"id": "vH0wTtXdRz5uGa8j",
"category": "XqgPq28Eo5VCFSZu",
"name": "Samples to include",
"param_name": "samples_to_include",
"description": "Comma-separated list of samples to include",
"help_text": "Leave blank to include all samples",
"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.",
"help_text": "Leaving this empty includes all samples.",
"type": "text",
"value_type": "string"
},
Expand All @@ -168,7 +169,7 @@
"category": "VisPCA",
"name": "Samples to rename",
"param_name": "samples_to_rename",
"description": "Sample renaming pairs: old_name:new_name",
"description": "Rename samples manually for display on the PCA plot. Use the format old_name:new_name.",
"help_text": "Separate multiple pairs with commas",
"type": "text",
"value_type": "string"
Expand All @@ -178,32 +179,18 @@
"category": "VisGeneral",
"name": "Colors for plots",
"param_name": "colors_for_plots",
"description": "Comma-separated colors for PCA and histogram. Defaults to the MOSuite palette.",
"description": "Optional colors for PCA, histogram, and heatmap plots. Colors must either be names in grDevices::colors() or valid hex codes. Unnamed colors are assigned by factor level order when the grouping column is a factor; otherwise, they follow the order in which groups first appear in the metadata column. If more groups are present than colors provided, supplied colors are used first and additional colors are generated from the selected palette for the remaining groups.",
"help_text": "Use color names or hex codes. Supplied colors are used first; if there are more groups than colors, additional colors are generated from the MOSuite palette, with random colors only if that palette is too short.",
"type": "text",
"value_type": "string",
"default_value": "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500"
},
{
"id": "vK3zWwAgUc8xJd1m",
"category": "VisPCA",
"name": "Add labels to PCA",
"param_name": "add_label_to_pca",
"description": "Label points on the PCA plot",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
"extra_data": [
"TRUE",
"FALSE"
]
},
{
"id": "vL4aXxBhVd9yKe2n",
"category": "VisPCA",
"name": "PCA component on x-axis",
"param_name": "principal_component_on_x_axis",
"description": "Principal component to plot on the x-axis",
"description": "The principal component to plot on the x-axis for the PCA plot. Choices include 1, 2, 3, and additional available components.",
"type": "text",
"value_type": "integer",
"default_value": "1"
Expand All @@ -213,7 +200,7 @@
"category": "VisPCA",
"name": "PCA component on y-axis",
"param_name": "principal_component_on_y_axis",
"description": "Principal component to plot on the y-axis",
"description": "The principal component to plot on the y-axis for the PCA plot. Choices include 1, 2, 3, and additional available components.",
"type": "text",
"value_type": "integer",
"default_value": "2"
Expand Down Expand Up @@ -272,14 +259,29 @@
"description": "Point size for the PCA plot",
"type": "text",
"value_type": "number",
"default_value": "3"
"default_value": "5"
},
{
"id": "vR0gDdHnBj5eQk8u",
"category": "VisPCA",
"name": "Add labels to PCA",
"param_name": "add_label_to_pca",
"description": "If TRUE, display labels from label_colname on PCA points. If FALSE, the PCA plot uses unlabeled points while heatmap labels still use label_colname.",
"help_text": "Set FALSE to remove labels from PCA points.",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
"extra_data": [
"TRUE",
"FALSE"
]
},
{
"id": "vS1hEeIoCk6fRl9u",
"category": "VisHistogram",
"name": "Color histogram by group",
"param_name": "color_histogram_by_group",
"description": "Color histogram by group instead of sample",
"description": "Set to FALSE to label histogram by Sample Names, or set to TRUE to label histogram by the column selected in the Group Column Used to Color Histogram parameter.",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
Expand All @@ -293,7 +295,7 @@
"category": "VisHistogram",
"name": "Set histogram x-axis min/max",
"param_name": "set_min_max_for_x_axis_for_histogram",
"description": "Set min/max value for histogram x-axis",
"description": "Whether to set minimum and maximum values for the histogram x-axis.",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
Expand All @@ -307,7 +309,7 @@
"category": "VisHistogram",
"name": "Histogram x-axis minimum",
"param_name": "minimum_for_x_axis_for_histogram",
"description": "x-axis minimum for histogram plot",
"description": "X-axis minimum for the histogram plot.",
"type": "text",
"value_type": "number",
"default_value": "-1"
Expand All @@ -317,7 +319,7 @@
"category": "VisHistogram",
"name": "Histogram x-axis maximum",
"param_name": "maximum_for_x_axis_for_histogram",
"description": "x-axis maximum for histogram plot",
"description": "X-axis maximum for the histogram plot.",
"type": "text",
"value_type": "number",
"default_value": "1"
Expand All @@ -327,7 +329,7 @@
"category": "VisHistogram",
"name": "Legend font size for histogram",
"param_name": "legend_font_size_for_histogram",
"description": "Legend font size for histogram plot. Leave blank to scale automatically.",
"description": "Legend font size for the histogram plot. When no value is supplied, the size is scaled automatically.",
"type": "text",
"value_type": "number",
"default_value": ""
Expand All @@ -337,7 +339,7 @@
"category": "VisHistogram",
"name": "Legend position for histogram",
"param_name": "legend_position_for_histogram",
"description": "Legend position for histogram plot",
"description": "Legend position for the histogram plot. Consider setting to none for a large number of samples.",
"type": "list",
"value_type": "string",
"default_value": "top",
Expand All @@ -353,7 +355,7 @@
"category": "VisHistogram",
"name": "Histogram legend columns",
"param_name": "number_of_histogram_legend_columns",
"description": "Number of columns for the histogram legend",
"description": "Number of columns for the histogram legend.",
"type": "text",
"value_type": "integer",
"default_value": "6"
Expand All @@ -363,7 +365,7 @@
"category": "VisGeneral",
"name": "Plot correlation heatmap",
"param_name": "plot_corr_matrix_heatmap",
"description": "Create a correlation matrix heatmap for sample similarity",
"description": "Datasets with a large number of samples may be too large to create a correlation matrix heatmap. If this function takes longer than 5 minutes to run, set to FALSE and the correlation matrix will not be created.",
"help_text": "Set to FALSE for datasets with many samples to avoid long run times",
"type": "list",
"value_type": "string",
Expand All @@ -378,7 +380,7 @@
"category": "VisGeneral",
"name": "Interactive plots",
"param_name": "interactive_plots",
"description": "Create interactive plots with plotly (PCA and histogram)",
"description": "Set to TRUE to make PCA and histogram plots interactive with plotly, allowing you to hover over a point or line to view sample information. The similarity heatmap will not display if this toggle is set to TRUE.",
"help_text": "Interactive plots allow hovering to view sample information, but correlation heatmap will not display",
"type": "list",
"value_type": "string",
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 (#10, @phoman14).
- Align plot color defaults with MOSuite package defaults (#4, @phoman14).
- Leave the histogram legend font size blank by default so MOSuite can scale long or numerous legend labels automatically (#4, @phoman14).
- Improve the Code Ocean app panel parameter selection and categories. (#3, @phoman14)
Expand Down
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