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kelly-sovacoolkelly-sovacool
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chore: Merge branch 'syncweaver' of github.com:NIDAP-Community/MOSuite-plot-pca-2D into syncweaver
2 parents 55465e4 + 9bc3ac3 commit 8b96b00

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Lines changed: 260 additions & 66 deletions

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‎.codeocean/app-panel.json‎

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}
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],
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"categories": [
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{
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"id": "7Rr6IxOMDucKMImp",
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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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},
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{
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"id": "EzTg1ivlFDHEy9PI",
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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": "FvI4Z2eb9sjL47Jt",
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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\udcca"
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},
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{
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"id": "7Rr6IxOMDucKMImp",
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"name": "Advanced",
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"description": "Advanced input data options",
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"icon": "\ud83d\udcc1"
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}
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],
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"parameters": [
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{
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"id": "count_type_id",
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"category": "FvI4Z2eb9sjL47Jt",
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"category": "EzTg1ivlFDHEy9PI",
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"name": "Count type",
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"param_name": "count_type",
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"description": "Type of counts to use (e.g., filt, norm)",
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"type": "list",
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"value_type": "string",
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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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"norm"
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]
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},
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{
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"id": "group_colname_id",
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"category": "EzTg1ivlFDHEy9PI",
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"name": "Group column name",
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"param_name": "group_colname",
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"description": "Column name for sample groups",
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"type": "text",
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"value_type": "string",
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"default_value": "Group"
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},
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{
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"id": "label_colname_id",
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"category": "EzTg1ivlFDHEy9PI",
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"name": "Label column name",
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"param_name": "label_colname",
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"description": "Column name for sample labels",
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"type": "text",
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"value_type": "string",
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"default_value": "filt"
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"default_value": "Label"
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},
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{
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"id": "sub_count_type_id",
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"category": "FvI4Z2eb9sjL47Jt",
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"category": "7Rr6IxOMDucKMImp",
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"name": "Sub count type",
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"param_name": "sub_count_type",
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"description": "Sub count type if count_type is a list",
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"type": "text",
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"value_type": "string"
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},
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{
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"id": "feature_id_colname_id",
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"category": "FvI4Z2eb9sjL47Jt",
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"name": "Feature ID column name",
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"param_name": "feature_id_colname",
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"description": "Column name for feature IDs",
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"type": "text",
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"value_type": "string"
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},
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{
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"id": "sample_id_colname_id",
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"category": "FvI4Z2eb9sjL47Jt",
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"category": "EzTg1ivlFDHEy9PI",
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"name": "Sample ID column name",
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"param_name": "sample_id_colname",
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"description": "Column name for sample IDs",
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"type": "text",
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"value_type": "string"
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},
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{
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"id": "group_colname_id",
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"category": "7Rr6IxOMDucKMImp",
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"name": "Group column name",
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"param_name": "group_colname",
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"description": "Column name for sample groups",
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"type": "text",
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"value_type": "string",
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"default_value": "Group"
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},
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{
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"id": "label_colname_id",
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"category": "7Rr6IxOMDucKMImp",
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"name": "Label column name",
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"param_name": "label_colname",
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"description": "Column name for sample labels",
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"type": "text",
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"value_type": "string",
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"default_value": "Label"
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},
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{
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"id": "principal_components_id",
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"category": "EzTg1ivlFDHEy9PI",
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"category": "7Rr6IxOMDucKMImp",
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"name": "Principal components",
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"param_name": "principal_components",
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"description": "Principal components to plot (comma-separated, e.g., 1,2)",
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"type": "text",
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"value_type": "string",
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"default_value": "1,2"
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},
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{
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"id": "feature_id_colname_id",
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"category": "7Rr6IxOMDucKMImp",
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"name": "Feature ID column name",
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"param_name": "feature_id_colname",
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"description": "Column name for feature IDs",
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"type": "text",
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"value_type": "string"
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},
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{
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"id": "legend_position_id",
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"category": "FvI4Z2eb9sjL47Jt",
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"name": "Legend position",
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"param_name": "legend_position",
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"description": "Position of the legend",
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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": "point_size_id",
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"description": "Size of points in plot",
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"type": "text",
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"value_type": "string",
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"default_value": "1"
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"default_value": "3"
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},
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{
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"id": "add_label_id",
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"category": "FvI4Z2eb9sjL47Jt",
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"name": "Add labels",
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"param_name": "add_label",
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"description": "Whether to add labels to points",
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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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"default_value": "TRUE",
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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": "label_font_size_id",
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"name": "Interactive plots",
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"param_name": "interactive_plots",
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"description": "Whether to create interactive plots",
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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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"default_value": "FALSE",
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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": "color_values_id",
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"category": "FvI4Z2eb9sjL47Jt",
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"name": "Color values",
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"param_name": "color_values",
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"description": "Comma-separated color values for groups",
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"description": "Comma-separated group colors. Defaults to the MOSuite palette.",
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"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.",
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"type": "text",
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"value_type": "string",
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"default_value": "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500"
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"file_name": "figures/pca/pca_2D.png"
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}
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]
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}
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}

‎.codeocean/environment.json‎

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{
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"version": 1,
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"base_image": "codeocean/mosuite:v0.3.0",
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"post_install": true,
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"base_image": "codeocean/mosuite-minimal:v0.3.2",
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"options": {
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"registry_host_arg": true,
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"git_ask_pass": true,

‎CHANGELOG.md‎

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# Code Ocean capsule - MOSuite - plot 2D PCA
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## Development version
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- Align the PCA color defaults with MOSuite package defaults (#2, @phoman14).
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- Document that color palettes fall back to random colors only when too few colors are provided (#2, @phoman14).
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- Improved the Code Ocean parameter UI for the plot pca 2D capsule (#1, @phoman14).
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- Use MOSuite v0.3.2. (#3, @kelly-sovacool)
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## v2.0
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- Use MOSuite v0.3.0
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Initial release
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<https://poc-nci.codeocean.io/capsule/8095429/tree/v1> `bd6ca75`
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<https://poc-nci.codeocean.io/capsule/8095429/tree/v1> `bd6ca75`

‎SECURITY.md‎

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# NCI Standard Public Repository Security Policy
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## Maintained Versions
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Actively maintained versions of contained software will vary from repository to repository, or may not be relevant at all.
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The developers of this repository will update this section if any actively maintained versions of the software need to be publicly disclosed. Otherwise, contact the developers directly for any version information.
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## Vulnerability Disclosure:
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### Option 1: HHS Vulnerability Disclosure
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Follow the instructions listed in the [HHS vulnerability disclosure policy](https://www.hhs.gov/vulnerability-disclosure-policy/index.html).
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### Option 2: Private Vulnerability Report
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1. Click on the **Security and quality** tab of this repository.
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2. Locate the **Report a vulnerability** button. If the button is not on the **Security and quality** landing page, look under the **Advisories** section in the side bar.
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3. Click the **Report a vulnerability** button and submit the form. The developers will receive a notification of your submission.
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‎code/MOSuite/inst/extdata/galaxy/galaxy.R‎

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arg_name <- template[[arg_type]][[i]]$key
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if (arg_name %in% names(func_meta$args)) {
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arg_meta <- template[[arg_type]][[i]]
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arg_meta$description <- safe_rd_to_md(func_meta$args[[arg_name]]$description)
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arg_meta$description <- safe_rd_to_md(
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func_meta$args[[arg_name]]$description
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)
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arg_meta$defaultValue <- func_meta$args[[arg_name]]$defaultValue
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args_in_template <- c(args_in_template, arg_name)
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new_template[[arg_type]][[

‎code/main.R‎

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parser$add_argument(
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"--point_size",
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type = "double",
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default = 1,
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default = 3,
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help = "Size of points in plot"
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)
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parser$add_argument(
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"--color_values",
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type = "character",
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default = "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500",
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help = "Comma-separated color values"
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help = "Comma-separated group colors. Defaults to the MOSuite palette. Extra group colors are generated when needed."
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)
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args <- parser$parse_args()

‎environment/Dockerfile‎

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# hash:sha256:16a54343c83446772895fc0c0b1e88a6dbd136fee70bcacffff7886f30541b82
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# hash:sha256:1cdaa95e13fff441e379b92105346562d0c6d704231dc19f198eec619b9b7511
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ARG REGISTRY_HOST
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FROM $REGISTRY_HOST/codeocean/mosuite:v0.3.0
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FROM $REGISTRY_HOST/codeocean/mosuite-minimal:v0.3.2
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ARG DEBIAN_FRONTEND=noninteractive
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ARG GIT_ASKPASS
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COPY git-askpass /
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COPY postInstall /
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RUN --mount=type=secret,id=secrets . /run/secrets/secrets \
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&& /postInstall
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COPY git-ask-pass /

‎environment/postInstall‎

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This file was deleted.

‎tests/test-setup.R‎

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testthat::test_that("test setup has expected capsule files", {
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repo_root <- normalizePath(file.path(testthat::test_path(), "..", ".."))
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testthat::expect_true(file.exists(file.path(repo_root, "code", "main.R")))
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testthat::expect_true(file.exists(file.path(repo_root, "code", "run")))
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testthat::expect_true(file.exists(file.path(
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repo_root,
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".codeocean",
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"app-panel.json"
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)))
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})

‎tests/testthat.R‎

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library(testthat)
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test_dir(file.path("tests", "testthat"))

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