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Standardize normalize output figures across MOSuite function calls #4

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bb263a2
Update boolean parameters to TRUE/FALSE list options
phoman14 Jun 29, 2026
9924f5a
Move count_type to first position in Basic category
phoman14 Jun 29, 2026
d966a4b
Update norm_type to list with voom option (default: voom)
phoman14 Jun 29, 2026
326eebd
Update voom_normalization_method to list with none, scale, quantile, …
phoman14 Jun 29, 2026
1cfda17
Update legend_position parameter(s) to list with top, bottom, left, r…
phoman14 Jun 29, 2026
27888ab
Match PCA point size default to filter capsule
phoman14 Jun 29, 2026
0848d3a
Split visualization parameters by plot type
phoman14 Jun 30, 2026
bd8763a
Align normalize capsule color defaults
phoman14 Jul 2, 2026
62c064b
Align plot color defaults
phoman14 Jul 2, 2026
8df5d2d
Align histogram legend font default
phoman14 Jul 2, 2026
9591d66
docs: update plot default changelog
phoman14 Jul 2, 2026
ad5500b
build: install FigOutSync package for normalize capsule
phoman14 Jul 6, 2026
9f859f3
docs: add changelog author attribution
phoman14 Jul 6, 2026
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179 changes: 121 additions & 58 deletions .codeocean/app-panel.json
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Expand Up @@ -16,46 +16,72 @@
"id": "gDLmTU36PrmD13RK",
"name": "Input Data Parameters",
"description": "Options for defining input data",
"icon": "📁"
"icon": "\ud83d\udcc1"
},
{
"id": "gn9FXwemlVazWQIo",
"name": "Basic",
"icon": "📂"
"icon": "\ud83d\udcc2"
},
{
"id": "VisGeneral",
"name": "Visualization: General",
"description": "General visualization and plotting options",
"icon": "\ud83d\udcca"
},
{
"id": "VisPCA",
"name": "Visualization: PCA",
"description": "PCA plot options",
"icon": "\ud83d\udcca"
},
{
"id": "VisHistogram",
"name": "Visualization: Histogram",
"description": "Histogram plot options",
"icon": "\ud83d\udcca"
},
{
"id": "VisHeatmap",
"name": "Visualization: Heatmap",
"description": "Heatmap plot options",
"icon": "\ud83d\udcca"
},
{
"id": "XqgPq28Eo5VCFSZu",
"name": "Advanced",
"description": "Advanced parameters",
"icon": "📂"
},
{
"id": "uQ7pLsNmVtR2cX9b",
"name": "Visualization",
"description": "Visualization and plotting options",
"icon": "📊"
"icon": "\ud83d\udcc2"
}
],
"parameters": [
{
"id": "UA4GuIpVAxdcmHAG",
"category": "XqgPq28Eo5VCFSZu",
"category": "gn9FXwemlVazWQIo",
"name": "Count type",
"param_name": "count_type",
"description": "Type of counts to normalize. Must be a count type in names(moo@counts)",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "filt"
"default_value": "filt",
"extra_data": [
"raw",
"clean",
"filt"
]
},
{
"id": "vA3pMmQwKs8nZx1c",
"category": "gn9FXwemlVazWQIo",
"name": "Normalization type",
"param_name": "norm_type",
"description": "Normalization type (default: voom)",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "voom"
"default_value": "voom",
"extra_data": [
"voom"
]
},
{
"id": "vB4qNnRxLt9oAy2d",
Expand All @@ -73,20 +99,29 @@
"name": "Input already log2",
"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",
"pattern": "TRUE|FALSE|T|F"
"extra_data": [
"TRUE",
"FALSE"
]
},
{
"id": "vD6sPpTzNv1qCw4f",
"category": "gn9FXwemlVazWQIo",
"name": "Voom normalization method",
"param_name": "voom_normalization_method",
"description": "Normalization method for limma::voom",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "quantile"
"default_value": "quantile",
"extra_data": [
"none",
"scale",
"quantile",
"cyclicloess"
]
},
{
"id": "vE7tQqUaOw2rDx5g",
Expand All @@ -110,7 +145,7 @@
},
{
"id": "vG9vSsWcQy4tFz7i",
"category": "XqgPq28Eo5VCFSZu",
"category": "VisGeneral",
"name": "Label column name",
"param_name": "label_colname",
"description": "Column from sample metadata containing labels for plots",
Expand Down Expand Up @@ -140,28 +175,32 @@
},
{
"id": "vJ2yVvZfTb7wIc0l",
"category": "XqgPq28Eo5VCFSZu",
"category": "VisGeneral",
"name": "Colors for plots",
"param_name": "colors_for_plots",
"description": "Comma-separated list of colors for PCA and histogram",
"help_text": "Use color names or hex codes. Leave blank to use defaults",
"description": "Comma-separated colors for PCA and histogram. Defaults to the MOSuite palette.",
"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"
"value_type": "string",
"default_value": "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500"
},
{
"id": "vK3zWwAgUc8xJd1m",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisPCA",
"name": "Add labels to PCA",
"param_name": "add_label_to_pca",
"description": "Label points on the PCA plot",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
"pattern": "TRUE|FALSE|T|F"
"extra_data": [
"TRUE",
"FALSE"
]
},
{
"id": "vL4aXxBhVd9yKe2n",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisPCA",
"name": "PCA component on x-axis",
"param_name": "principal_component_on_x_axis",
"description": "Principal component to plot on the x-axis",
Expand All @@ -171,7 +210,7 @@
},
{
"id": "vM5bYyCiWe0zLf3o",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisPCA",
"name": "PCA component on y-axis",
"param_name": "principal_component_on_y_axis",
"description": "Principal component to plot on the y-axis",
Expand All @@ -181,17 +220,23 @@
},
{
"id": "vN6cZzDjXf1aMg4p",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisPCA",
"name": "Legend position for PCA",
"param_name": "legend_position_for_pca",
"description": "Legend position for the PCA plot",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "top"
"default_value": "top",
"extra_data": [
"top",
"bottom",
"left",
"right"
]
},
{
"id": "vO7dAaEkYg2bNh5q",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisPCA",
"name": "Label offset x",
"param_name": "label_offset_x_",
"description": "Label offset x for the PCA plot",
Expand All @@ -201,7 +246,7 @@
},
{
"id": "vP8eBbFlZh3cOi6r",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisPCA",
"name": "Label offset y",
"param_name": "label_offset_y_",
"description": "Label offset y for the PCA plot",
Expand All @@ -211,7 +256,7 @@
},
{
"id": "vQ9fCcGmAi4dPj7s",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisPCA",
"name": "Label font size",
"param_name": "label_font_size",
"description": "Label font size for the PCA plot",
Expand All @@ -221,39 +266,45 @@
},
{
"id": "vR0gDdHnBj5eQk8t",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisPCA",
"name": "Point size for PCA",
"param_name": "point_size_for_pca",
"description": "Point size for the PCA plot",
"type": "text",
"value_type": "number",
"default_value": "8"
"default_value": "3"
},
{
"id": "vS1hEeIoCk6fRl9u",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisHistogram",
"name": "Color histogram by group",
"param_name": "color_histogram_by_group",
"description": "Color histogram by group instead of sample",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
"pattern": "TRUE|FALSE|T|F"
"extra_data": [
"TRUE",
"FALSE"
]
},
{
"id": "vT2iFfJpDl7gSm0v",
"category": "uQ7pLsNmVtR2cX9b",
"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",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
"pattern": "TRUE|FALSE|T|F"
"extra_data": [
"TRUE",
"FALSE"
]
},
{
"id": "vU3jGgKqEm8hTn1w",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisHistogram",
"name": "Histogram x-axis minimum",
"param_name": "minimum_for_x_axis_for_histogram",
"description": "x-axis minimum for histogram plot",
Expand All @@ -263,7 +314,7 @@
},
{
"id": "vV4kHhLrFn9iUo2x",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisHistogram",
"name": "Histogram x-axis maximum",
"param_name": "maximum_for_x_axis_for_histogram",
"description": "x-axis maximum for histogram plot",
Expand All @@ -273,27 +324,33 @@
},
{
"id": "vW5lIiMsGo0jVp3y",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisHistogram",
"name": "Legend font size for histogram",
"param_name": "legend_font_size_for_histogram",
"description": "Legend font size for histogram plot",
"description": "Legend font size for histogram plot. Leave blank to scale automatically.",
"type": "text",
"value_type": "number",
"default_value": "10"
"default_value": ""
},
{
"id": "vX6mJjNtHp1kWq4z",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisHistogram",
"name": "Legend position for histogram",
"param_name": "legend_position_for_histogram",
"description": "Legend position for histogram plot",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "top"
"default_value": "top",
"extra_data": [
"top",
"bottom",
"left",
"right"
]
},
{
"id": "vY7nKkOuIq2lXr5a",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisHistogram",
"name": "Histogram legend columns",
"param_name": "number_of_histogram_legend_columns",
"description": "Number of columns for the histogram legend",
Expand All @@ -303,27 +360,33 @@
},
{
"id": "vZ8oLlPvJr3mYs6b",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisGeneral",
"name": "Plot correlation heatmap",
"param_name": "plot_corr_matrix_heatmap",
"description": "Create a correlation matrix heatmap for sample similarity",
"help_text": "Set to FALSE for datasets with many samples to avoid long run times",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "TRUE",
"pattern": "TRUE|FALSE|T|F"
"extra_data": [
"TRUE",
"FALSE"
]
},
{
"id": "wA9pMmQwKs4nZt7c",
"category": "uQ7pLsNmVtR2cX9b",
"category": "VisGeneral",
"name": "Interactive plots",
"param_name": "interactive_plots",
"description": "Create interactive plots with plotly (PCA and histogram)",
"help_text": "Interactive plots allow hovering to view sample information, but correlation heatmap will not display",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "FALSE",
"pattern": "TRUE|FALSE|T|F"
"extra_data": [
"TRUE",
"FALSE"
]
}
],
"results": [
Expand All @@ -337,4 +400,4 @@
"file_name": "figures/norm/voom/pca.png"
}
]
}
}
6 changes: 6 additions & 0 deletions CHANGELOG.md
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@@ -1,5 +1,11 @@
# Code Ocean capsule - MOSuite - normalize counts

## Development version

- Install MOSuite from the `FigOutSync` package branch during capsule setup so the capsule uses the updated figure-standardization behavior before the next release image is available (#4, @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).

## v3.0

- Use the MOSuite v0.3.0 docker image.
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