<commit_before>Ext.namespace('Gemma');

Gemma.MetaVisualizationConfig = {};

// Sizes
Gemma.MetaVisualizationConfig.cellWidth = 14;
Gemma.MetaVisualizationConfig.cellHeight = 10;
Gemma.MetaVisualizationConfig.groupSeparatorHeight = 4;
Gemma.MetaVisualizationConfig.columnSeparatorWidth = 1;
Gemma.MetaVisualizationConfig.groupSeparatorWidth = 4;
Gemma.MetaVisualizationConfig.geneLabelFontSize = 9;
Gemma.MetaVisualizationConfig.columnLabelFontSize = 9;

Gemma.MetaVisualizationConfig.labelAngle = 315.0;
Gemma.MetaVisualizationConfig.labelBaseYCoor = 196;
Gemma.MetaVisualizationConfig.columnLabelHeight = 210;

Gemma.MetaVisualizationConfig.minAppHeight = 600;
Gemma.MetaVisualizationConfig.minAppWidth = 600;
Gemma.MetaVisualizationConfig.windowPadding = 50;
Gemma.MetaVisualizationConfig.toolPanelWidth = 300;

Gemma.MetaVisualizationConfig.labelExtraSpace = Math.floor(Gemma.MetaVisualizationConfig.labelBaseYCoor / Math.tan((360 - Gemma.MetaVisualizationConfig.labelAngle) * Math.PI / 180));

// Colors
Gemma.MetaVisualizationConfig.cellHighlightColor = 'red';
Gemma.MetaVisualizationConfig.defaultLabelColor = 'black';
Gemma.MetaVisualizationConfig.geneLabelHighlightColor = 'red';
Gemma.MetaVisualizationConfig.rowHighlightColor = 'pink';
Gemma.MetaVisualizationConfig.rowCellSelectColor = 'pink';
Gemma.MetaVisualizationConfig.columnHighlightColor = 'pink';
Gemma.MetaVisualizationConfig.analysisLabelHighlightColor = 'rgb(255,140,0)';
Gemma.MetaVisualizationConfig.baselineFactorValueColor = 'rgb(128, 0, 0)';
Gemma.MetaVisualizationConfig.factorValueDefaultColor = 'rgb(0,0,200)';
Gemma.MetaVisualizationConfig.analysisLabelBackgroundColor1 = 'rgba(10,100,10, 0.1)';
Gemma.MetaVisualizationConfig.analysisLabelBackgroundColor2 = 'rgba(10,100,10, 0.05)';

Gemma.MetaVisualizationConfig.miniPieColor = 'rgb(95,158,160)';
Gemma.MetaVisualizationConfig.miniPieColorInvalid = 'rgb(192,192,192)';

Gemma.MetaVisualizationConfig.basicColourRange = new org.systemsbiology.visualization.DiscreteColorRange(20, {
			min : -1,
			max : 1
		}, {
			maxColor : {
				r : 255,
				g : 215,
				b : 0,
				a : 1
			},
			minColor : {
				r : 255,
				g : 255,
				b : 0,
				a : 1
			},
			emptyDataColor : {
				r : 100,
				g : 100,
				b : 100,
				a : 0.8
			},
			passThroughBlack : true
		});

Gemma.MetaVisualizationConfig.contrastsColourRange = new org.systemsbiology.visualization.DiscreteColorRange(20, {
			min : -3,
			max : 3
		}, {
			maxColor : {
				r : 0,
				g : 255,
				b : 0,
				a : 1
			},
			minColor : {
				r : 255,
				g : 0,
				b : 255,
				a : 1
			},
			emptyDataColor : {
				r : 100,
				g : 100,
				b : 100,
				a : 0.8
			},
			passThroughBlack : true
		});<commit_msg>colours for fold change; could use more colour blindness proofing<commit_after>Ext.namespace('Gemma');

Gemma.MetaVisualizationConfig = {};

// Sizes
Gemma.MetaVisualizationConfig.cellWidth = 14;
Gemma.MetaVisualizationConfig.cellHeight = 10;
Gemma.MetaVisualizationConfig.groupSeparatorHeight = 4;
Gemma.MetaVisualizationConfig.columnSeparatorWidth = 1;
Gemma.MetaVisualizationConfig.groupSeparatorWidth = 4;
Gemma.MetaVisualizationConfig.geneLabelFontSize = 9;
Gemma.MetaVisualizationConfig.columnLabelFontSize = 9;

Gemma.MetaVisualizationConfig.labelAngle = 315.0;
Gemma.MetaVisualizationConfig.labelBaseYCoor = 196;
Gemma.MetaVisualizationConfig.columnLabelHeight = 210;

Gemma.MetaVisualizationConfig.minAppHeight = 600;
Gemma.MetaVisualizationConfig.minAppWidth = 600;
Gemma.MetaVisualizationConfig.windowPadding = 50;
Gemma.MetaVisualizationConfig.toolPanelWidth = 300;

Gemma.MetaVisualizationConfig.labelExtraSpace = Math.floor(Gemma.MetaVisualizationConfig.labelBaseYCoor / Math.tan((360 - Gemma.MetaVisualizationConfig.labelAngle) * Math.PI / 180));

// Colors
Gemma.MetaVisualizationConfig.cellHighlightColor = 'red';
Gemma.MetaVisualizationConfig.defaultLabelColor = 'black';
Gemma.MetaVisualizationConfig.geneLabelHighlightColor = 'red';
Gemma.MetaVisualizationConfig.rowHighlightColor = 'pink';
Gemma.MetaVisualizationConfig.rowCellSelectColor = 'pink';
Gemma.MetaVisualizationConfig.columnHighlightColor = 'pink';
Gemma.MetaVisualizationConfig.analysisLabelHighlightColor = 'rgb(255,140,0)';
Gemma.MetaVisualizationConfig.baselineFactorValueColor = 'rgb(128, 0, 0)';
Gemma.MetaVisualizationConfig.factorValueDefaultColor = 'rgb(0,0,200)';
Gemma.MetaVisualizationConfig.analysisLabelBackgroundColor1 = 'rgba(10,100,10, 0.1)';
Gemma.MetaVisualizationConfig.analysisLabelBackgroundColor2 = 'rgba(10,100,10, 0.05)';

Gemma.MetaVisualizationConfig.miniPieColor = 'rgb(95,158,160)';
Gemma.MetaVisualizationConfig.miniPieColorInvalid = 'rgb(192,192,192)';

Gemma.MetaVisualizationConfig.basicColourRange = new org.systemsbiology.visualization.DiscreteColorRange(20, {
			min : -1,
			max : 1
		}, {
			maxColor : {
				r : 255,
				g : 215,
				b : 0,
				a : 1
			},
			minColor : {
				r : 255,
				g : 255,
				b : 0,
				a : 1
			},
			emptyDataColor : {
				r : 100,
				g : 100,
				b : 100,
				a : 0.8
			},
			passThroughBlack : true
		});

Gemma.MetaVisualizationConfig.contrastsColourRange = new org.systemsbiology.visualization.DiscreteColorRange(20, {
			min : -3,
			max : 3
		}, {
			maxColor : {
				r : 0,
				g : 255,
				b : 255,
				a : 1
			},
			minColor : {
				r : 255,
				g : 0,
				b : 255,
				a : 1
			},
			emptyDataColor : {
				r : 100,
				g : 100,
				b : 100,
				a : 0.8
			},
			passThroughBlack : true
		});
{'fraction_non_alphanumeric': 0.11528592375366568, 'fraction_numerical': 0.05571847507331378, 'mean_word_length': 4.52327935222672, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '684611', 'n_tokens_mistral': 2386, 'n_tokens_neox': 1886, 'n_words': 289}