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phoman14kelly-sovacool
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kelly-sovacool
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feat(app-panel): improve Code Ocean parameters & categories (#3)
* Update boolean parameters to TRUE/FALSE list options * Move count_type to first position in Basic category * Update norm_type to list with voom option (default: voom) * Update voom_normalization_method to list with none, scale, quantile, cyclicloess (default: quantile) * Update legend_position parameter(s) to list with top, bottom, left, right options * Match PCA point size default to filter capsule * Split visualization parameters by plot type * Move Advanced category to end * Move normalization type before method * docs: update changelog --------- Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>
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Lines changed: 130 additions & 64 deletions

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‎.codeocean/app-panel.json‎

Lines changed: 124 additions & 62 deletions
Original file line numberDiff line numberDiff line change
@@ -16,46 +16,59 @@
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"id": "gDLmTU36PrmD13RK",
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"name": "Input Data Parameters",
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"description": "Options for defining input data",
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"icon": "📁"
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"icon": "\ud83d\udcc1"
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},
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{
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"id": "gn9FXwemlVazWQIo",
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"name": "Basic",
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"icon": "📂"
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"icon": "\ud83d\udcc2"
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},
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{
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"id": "VisGeneral",
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"name": "Visualization: General",
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"description": "General visualization and plotting options",
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"icon": "\ud83d\udcca"
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},
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{
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"id": "VisPCA",
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"name": "Visualization: PCA",
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"description": "PCA plot options",
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"icon": "\ud83d\udcca"
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},
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{
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"id": "VisHistogram",
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"name": "Visualization: Histogram",
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"description": "Histogram plot options",
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"icon": "\ud83d\udcca"
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},
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{
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"id": "VisHeatmap",
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"name": "Visualization: Heatmap",
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"description": "Heatmap plot options",
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"icon": "\ud83d\udcca"
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},
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{
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"id": "XqgPq28Eo5VCFSZu",
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"name": "Advanced",
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"description": "Advanced parameters",
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"icon": "📂"
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},
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{
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"id": "uQ7pLsNmVtR2cX9b",
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"name": "Visualization",
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"description": "Visualization and plotting options",
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"icon": "📊"
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"icon": "\ud83d\udcc2"
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}
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],
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"parameters": [
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{
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"id": "UA4GuIpVAxdcmHAG",
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"category": "XqgPq28Eo5VCFSZu",
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"category": "gn9FXwemlVazWQIo",
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"name": "Count type",
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"param_name": "count_type",
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"description": "Type of counts to normalize. Must be a count type in names(moo@counts)",
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"type": "text",
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"value_type": "string",
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"default_value": "filt"
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},
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{
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"id": "vA3pMmQwKs8nZx1c",
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"category": "gn9FXwemlVazWQIo",
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"name": "Normalization type",
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"param_name": "norm_type",
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"description": "Normalization type (default: voom)",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "voom"
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"default_value": "filt",
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"extra_data": [
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"raw",
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"clean",
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"filt"
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]
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},
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{
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"id": "vB4qNnRxLt9oAy2d",
@@ -73,20 +86,42 @@
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"name": "Input already log2",
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"param_name": "input_in_log_counts",
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"description": "Set TRUE if counts are already log2-transformed",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "FALSE",
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"pattern": "TRUE|FALSE|T|F"
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"extra_data": [
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"TRUE",
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"FALSE"
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]
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},
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{
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"id": "vA3pMmQwKs8nZx1c",
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"category": "gn9FXwemlVazWQIo",
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"name": "Normalization type",
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"param_name": "norm_type",
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"description": "Normalization type (default: voom)",
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"type": "list",
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"value_type": "string",
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"default_value": "voom",
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"extra_data": [
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"voom"
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]
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},
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{
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"id": "vD6sPpTzNv1qCw4f",
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"category": "gn9FXwemlVazWQIo",
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"name": "Voom normalization method",
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"param_name": "voom_normalization_method",
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"description": "Normalization method for limma::voom",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "quantile"
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"default_value": "quantile",
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"extra_data": [
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"none",
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"scale",
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"quantile",
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"cyclicloess"
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]
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},
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{
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"id": "vE7tQqUaOw2rDx5g",
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},
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{
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"id": "vG9vSsWcQy4tFz7i",
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"category": "XqgPq28Eo5VCFSZu",
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"category": "VisGeneral",
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"name": "Label column name",
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"param_name": "label_colname",
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"description": "Column from sample metadata containing labels for plots",
@@ -130,7 +165,7 @@
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},
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{
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"id": "vI1xUuYeSa6vHb9k",
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"category": "XqgPq28Eo5VCFSZu",
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"category": "VisPCA",
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"name": "Samples to rename",
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"param_name": "samples_to_rename",
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"description": "Sample renaming pairs: old_name:new_name",
@@ -140,7 +175,7 @@
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},
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{
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"id": "vJ2yVvZfTb7wIc0l",
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"category": "XqgPq28Eo5VCFSZu",
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"category": "VisGeneral",
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"name": "Colors for plots",
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"param_name": "colors_for_plots",
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"description": "Comma-separated list of colors for PCA and histogram",
@@ -150,18 +185,21 @@
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},
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{
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"id": "vK3zWwAgUc8xJd1m",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisPCA",
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"name": "Add labels to PCA",
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"param_name": "add_label_to_pca",
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"description": "Label points on the PCA plot",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "TRUE",
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"pattern": "TRUE|FALSE|T|F"
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"extra_data": [
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"TRUE",
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"FALSE"
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]
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},
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{
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"id": "vL4aXxBhVd9yKe2n",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisPCA",
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"name": "PCA component on x-axis",
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"param_name": "principal_component_on_x_axis",
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"description": "Principal component to plot on the x-axis",
@@ -171,7 +209,7 @@
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},
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{
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"id": "vM5bYyCiWe0zLf3o",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisPCA",
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"name": "PCA component on y-axis",
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"param_name": "principal_component_on_y_axis",
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"description": "Principal component to plot on the y-axis",
@@ -181,17 +219,23 @@
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},
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{
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"id": "vN6cZzDjXf1aMg4p",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisPCA",
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"name": "Legend position for PCA",
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"param_name": "legend_position_for_pca",
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"description": "Legend position for the PCA plot",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "top"
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"default_value": "top",
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"extra_data": [
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"top",
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"bottom",
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"left",
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"right"
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]
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},
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{
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"id": "vO7dAaEkYg2bNh5q",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisPCA",
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"name": "Label offset x",
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"param_name": "label_offset_x_",
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"description": "Label offset x for the PCA plot",
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},
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{
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"id": "vP8eBbFlZh3cOi6r",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisPCA",
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"name": "Label offset y",
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"param_name": "label_offset_y_",
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"description": "Label offset y for the PCA plot",
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},
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{
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"id": "vQ9fCcGmAi4dPj7s",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisPCA",
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"name": "Label font size",
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"param_name": "label_font_size",
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"description": "Label font size for the PCA plot",
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},
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{
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"id": "vR0gDdHnBj5eQk8t",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisPCA",
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"name": "Point size for PCA",
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"param_name": "point_size_for_pca",
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"description": "Point size for the PCA plot",
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"type": "text",
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"value_type": "number",
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"default_value": "8"
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"default_value": "1"
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},
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{
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"id": "vS1hEeIoCk6fRl9u",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisHistogram",
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"name": "Color histogram by group",
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"param_name": "color_histogram_by_group",
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"description": "Color histogram by group instead of sample",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "TRUE",
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"pattern": "TRUE|FALSE|T|F"
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"extra_data": [
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"TRUE",
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"FALSE"
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]
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},
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{
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"id": "vT2iFfJpDl7gSm0v",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisHistogram",
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"name": "Set histogram x-axis min/max",
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"param_name": "set_min_max_for_x_axis_for_histogram",
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"description": "Set min/max value for histogram x-axis",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "FALSE",
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"pattern": "TRUE|FALSE|T|F"
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"extra_data": [
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"TRUE",
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"FALSE"
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]
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},
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{
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"id": "vU3jGgKqEm8hTn1w",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisHistogram",
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"name": "Histogram x-axis minimum",
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"param_name": "minimum_for_x_axis_for_histogram",
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"description": "x-axis minimum for histogram plot",
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},
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{
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"id": "vV4kHhLrFn9iUo2x",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisHistogram",
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"name": "Histogram x-axis maximum",
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"param_name": "maximum_for_x_axis_for_histogram",
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"description": "x-axis maximum for histogram plot",
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},
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{
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"id": "vW5lIiMsGo0jVp3y",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisHistogram",
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"name": "Legend font size for histogram",
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"param_name": "legend_font_size_for_histogram",
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"description": "Legend font size for histogram plot",
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},
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{
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"id": "vX6mJjNtHp1kWq4z",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisHistogram",
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"name": "Legend position for histogram",
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"param_name": "legend_position_for_histogram",
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"description": "Legend position for histogram plot",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "top"
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"default_value": "top",
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"extra_data": [
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"top",
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"bottom",
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"left",
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"right"
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]
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},
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{
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"id": "vY7nKkOuIq2lXr5a",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisHistogram",
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"name": "Histogram legend columns",
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"param_name": "number_of_histogram_legend_columns",
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"description": "Number of columns for the histogram legend",
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},
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{
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"id": "vZ8oLlPvJr3mYs6b",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisGeneral",
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"name": "Plot correlation heatmap",
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"param_name": "plot_corr_matrix_heatmap",
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"description": "Create a correlation matrix heatmap for sample similarity",
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"help_text": "Set to FALSE for datasets with many samples to avoid long run times",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "TRUE",
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"pattern": "TRUE|FALSE|T|F"
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"extra_data": [
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"TRUE",
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"FALSE"
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]
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},
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{
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"id": "wA9pMmQwKs4nZt7c",
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"category": "uQ7pLsNmVtR2cX9b",
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"category": "VisGeneral",
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"name": "Interactive plots",
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"param_name": "interactive_plots",
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"description": "Create interactive plots with plotly (PCA and histogram)",
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"help_text": "Interactive plots allow hovering to view sample information, but correlation heatmap will not display",
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"type": "text",
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"type": "list",
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"value_type": "string",
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"default_value": "FALSE",
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"pattern": "TRUE|FALSE|T|F"
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"extra_data": [
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"TRUE",
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"FALSE"
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]
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}
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],
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"results": [
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"file_name": "figures/norm/voom/pca.png"
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}
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]
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}
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}

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