@ggterm/core 0.2.17 → 0.3.0

package/dist/geoms/ma.d.ts

@@ -0,0 +1,77 @@
+/**
+ * geom_ma - MA plot for differential expression analysis
+ *
+ * Visualizes log fold change (M) vs average expression (A), commonly used
+ * alongside volcano plots in genomics. Shows intensity-dependent expression
+ * changes and helps identify biases in differential expression data.
+ *
+ * M = log2(fold change) = log2(condition1) - log2(condition2)
+ * A = average expression = (log2(condition1) + log2(condition2)) / 2
+ *
+ * @example
+ * ```ts
+ * // Basic MA plot
+ * gg(deResults)
+ *   .aes({ x: 'baseMean', y: 'log2FoldChange', label: 'gene' })
+ *   .geom(geom_ma())
+ *
+ * // With custom thresholds and labels
+ * gg(deResults)
+ *   .aes({ x: 'avgExpr', y: 'log2FC', label: 'symbol' })
+ *   .geom(geom_ma({
+ *     fc_threshold: 1.5,
+ *     p_col: 'padj',
+ *     p_threshold: 0.01,
+ *     n_labels: 10,
+ *   }))
+ * ```
+ */
+import type { Geom } from '../types';
+export interface MAOptions {
+    /** Log2 fold change threshold for coloring (default: 1, meaning 2-fold) */
+    fc_threshold?: number;
+    /** P-value threshold for significance coloring (default: 0.05) */
+    p_threshold?: number;
+    /** Column name containing p-values for significance (default: uses fc_threshold only) */
+    p_col?: string;
+    /** Whether x-axis (A) is already log2 transformed (default: false, will transform) */
+    x_is_log2?: boolean;
+    /** Color for up-regulated points (default: '#e41a1c' - red) */
+    up_color?: string;
+    /** Color for down-regulated points (default: '#377eb8' - blue) */
+    down_color?: string;
+    /** Color for non-significant points (default: '#999999' - gray) */
+    ns_color?: string;
+    /** Show M=0 baseline (default: true) */
+    show_baseline?: boolean;
+    /** Show fold change threshold lines (default: true) */
+    show_thresholds?: boolean;
+    /** Line type for reference lines (default: 'dashed') */
+    linetype?: 'solid' | 'dashed' | 'dotted';
+    /** Number of top significant points to label (default: 0, no labels) */
+    n_labels?: number;
+    /** Point size (default: 1) */
+    size?: number;
+    /** Point opacity (default: 0.6) */
+    alpha?: number;
+    /** Point character (default: '●') */
+    point_char?: string;
+    /** Show LOESS/lowess smoothing line (default: false) */
+    show_smooth?: boolean;
+}
+/**
+ * Create an MA plot for differential expression visualization
+ *
+ * Data should contain:
+ * - x column: average expression (A) - baseMean, avgExpr, or AveExpr
+ * - y column: log2 fold change (M) - log2FoldChange, log2FC, or logFC
+ * - label column (optional): gene names for labeling top hits
+ * - p-value column (optional): for significance-based coloring
+ *
+ * Points are classified as:
+ * - Up-regulated: M > fc_threshold (AND p < p_threshold if p_col specified)
+ * - Down-regulated: M < -fc_threshold (AND p < p_threshold if p_col specified)
+ * - Not significant: everything else
+ */
+export declare function geom_ma(options?: MAOptions): Geom;
+//# sourceMappingURL=ma.d.ts.map

package/dist/geoms/ma.d.ts.map

@@ -0,0 +1 @@
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package/dist/geoms/manhattan.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Manhattan Plot Geometry
+ *
+ * Visualizes GWAS (Genome-Wide Association Study) results with genomic position
+ * on the x-axis and -log10(p-value) on the y-axis. Points are colored by chromosome
+ * and significant associations are highlighted.
+ */
+import type { Geom } from '../types';
+export interface ManhattanOptions {
+    suggestive_threshold?: number;
+    genome_wide_threshold?: number;
+    chr_col?: string;
+    pos_col?: string;
+    p_col?: string;
+    y_is_neglog10?: boolean;
+    chr_colors?: string[];
+    highlight_color?: string;
+    suggestive_color?: string;
+    show_thresholds?: boolean;
+    threshold_linetype?: string;
+    n_labels?: number;
+    label_col?: string;
+    size?: number;
+    alpha?: number;
+    point_char?: string;
+    chr_gap?: number;
+}
+export declare function geom_manhattan(options?: ManhattanOptions): Geom;
+//# sourceMappingURL=manhattan.d.ts.map

package/dist/geoms/manhattan.d.ts.map

@@ -0,0 +1 @@
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package/dist/geoms/qq.d.ts

@@ -1,75 +1,67 @@
 /**
- * geom_qq - Q-Q plot geometry
+ * Q-Q Plot Geometry
  *
- * Creates Q-Q (quantile-quantile) plots to assess whether data
- * follows a particular distribution (typically normal).
+ * Creates quantile-quantile plots for comparing data distributions
+ * against theoretical distributions or other samples.
  *
  * @example
- * ```ts
- * // Basic Q-Q plot to check normality
+ * // Basic Q-Q plot against normal distribution
  * gg(data)
- *   .aes({ x: 'values' })
+ *   .aes({ sample: 'values' })
  *   .geom(geom_qq())
- *   .geom(geom_qq_line())
  *
- * // With custom distribution
+ * @example
+ * // Q-Q plot with reference line
  * gg(data)
- *   .aes({ x: 'values' })
- *   .geom(geom_qq({ distribution: 'uniform' }))
- * ```
+ *   .aes({ sample: 'values' })
+ *   .geom(geom_qq({ show_line: true }))
+ *
+ * @example
+ * // Q-Q plot with confidence band
+ * gg(data)
+ *   .aes({ sample: 'values' })
+ *   .geom(geom_qq({ show_ci: true, conf_level: 0.95 }))
  */
 import type { Geom } from '../types';
 export interface QQOptions {
-    /** Distribution to compare against (default: 'norm') */
-    distribution?: 'norm' | 'uniform' | 'exp';
-    /** Distribution parameters */
-    dparams?: {
-        mean?: number;
-        sd?: number;
-        rate?: number;
-    };
-    /** Point size */
-    size?: number;
-    /** Point shape */
-    shape?: string;
-    /** Point color */
-    color?: string;
-    /** Alpha transparency */
-    alpha?: number;
-}
-export interface QQLineOptions {
-    /** Distribution to compare against (default: 'norm') */
-    distribution?: 'norm' | 'uniform' | 'exp';
-    /** Distribution parameters */
-    dparams?: {
-        mean?: number;
-        sd?: number;
-        rate?: number;
-    };
-    /** Line color */
-    color?: string;
-    /** Line type */
-    linetype?: 'solid' | 'dashed' | 'dotted';
-    /** Alpha transparency */
-    alpha?: number;
+    /**
+     * Distribution to compare against
+     * @default 'normal'
+     */
+    distribution?: 'normal' | 'uniform' | 'exponential';
+    /**
+     * Show reference line (y = x for perfect fit)
+     * @default true
+     */
+    show_line?: boolean;
+    /**
+     * Show confidence band around reference line
+     * @default false
+     */
+    show_ci?: boolean;
+    /**
+     * Confidence level for CI band
+     * @default 0.95
+     */
+    conf_level?: number;
+    /**
+     * Line color for reference line
+     * @default '#ff0000'
+     */
+    line_color?: string;
+    /**
+     * Point character
+     * @default '●'
+     */
+    point_char?: string;
+    /**
+     * Use standardized residuals
+     * @default true
+     */
+    standardize?: boolean;
 }
 /**
- * Q-Q plot points
- *
- * Plots sample quantiles against theoretical quantiles.
- * If the points fall approximately on the diagonal reference line,
- * the data follows the reference distribution.
- *
- * The x aesthetic should be the variable to test.
- * Output uses x = theoretical quantile, y = sample quantile.
+ * Create a Q-Q plot geometry
  */
 export declare function geom_qq(options?: QQOptions): Geom;
-/**
- * Q-Q plot reference line
- *
- * Draws a line through the first and third quartiles of the
- * theoretical vs sample distribution. Points should fall on
- * this line if the data follows the reference distribution.
- */
-export declare function geom_qq_line(options?: QQLineOptions): Geom;
 //# sourceMappingURL=qq.d.ts.map

package/dist/geoms/qq.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"qq.d.ts","sourceRoot":"","sources":["../../src/geoms/qq.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AAEH,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AAErC,MAAM,WAAW,SAAS;IACxB;;;OAGG;IACH,YAAY,CAAC,EAAE,QAAQ,GAAG,SAAS,GAAG,aAAa,CAAC;IAEpD;;;OAGG;IACH,SAAS,CAAC,EAAE,OAAO,CAAC;IAEpB;;;OAGG;IACH,OAAO,CAAC,EAAE,OAAO,CAAC;IAElB;;;OAGG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;IAEpB;;;OAGG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;IAEpB;;;OAGG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;IAEpB;;;OAGG;IACH,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AAED;;GAEG;AACH,wBAAgB,OAAO,CAAC,OAAO,GAAE,SAAc,GAAG,IAAI,CAerD"}

package/dist/geoms/roc.d.ts

@@ -0,0 +1,44 @@
+/**
+ * ROC Curve Geom
+ *
+ * Creates Receiver Operating Characteristic curves for classifier evaluation.
+ * Plots sensitivity (true positive rate) vs 1-specificity (false positive rate).
+ *
+ * Expected data format:
+ * - fpr: False positive rate (1 - specificity), or x values
+ * - tpr: True positive rate (sensitivity), or y values
+ * - threshold (optional): Classification thresholds
+ * - model (optional): Model identifier for comparing multiple classifiers
+ *
+ * @example
+ * ```typescript
+ * gg(rocData)
+ *   .aes({ x: 'fpr', y: 'tpr', color: 'model' })
+ *   .geom(geom_roc({ show_auc: true, show_diagonal: true }))
+ * ```
+ */
+import type { Geom } from '../types';
+export interface RocOptions {
+    /** Show diagonal reference line (random classifier) (default: true) */
+    show_diagonal?: boolean;
+    /** Color for diagonal line (default: '#888888') */
+    diagonal_color?: string;
+    /** Line style for diagonal (default: 'dashed') */
+    diagonal_type?: 'solid' | 'dashed' | 'dotted';
+    /** Show AUC value in legend/annotation (default: true) */
+    show_auc?: boolean;
+    /** Show optimal threshold point (Youden's J) (default: false) */
+    show_optimal?: boolean;
+    /** Character for optimal point (default: '●') */
+    optimal_char?: string;
+    /** Show confidence band (default: false) */
+    show_ci?: boolean;
+    /** Confidence level (default: 0.95) */
+    conf_level?: number;
+    /** Fill area under curve (default: false) */
+    fill_auc?: boolean;
+    /** Fill opacity (default: 0.3) */
+    fill_alpha?: number;
+}
+export declare function geom_roc(options?: RocOptions): Geom;
+//# sourceMappingURL=roc.d.ts.map

package/dist/geoms/roc.d.ts.map

@@ -0,0 +1 @@
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package/dist/geoms/scree.d.ts

@@ -0,0 +1,97 @@
+/**
+ * Scree Plot Geometry
+ *
+ * Creates scree plots for PCA/factor analysis showing variance
+ * explained by each component.
+ *
+ * @example
+ * // Basic scree plot
+ * gg(data)
+ *   .aes({ x: 'component', y: 'variance' })
+ *   .geom(geom_scree())
+ *
+ * @example
+ * // Scree plot with cumulative variance
+ * gg(data)
+ *   .aes({ x: 'component', y: 'variance' })
+ *   .geom(geom_scree({ show_cumulative: true }))
+ *
+ * @example
+ * // Scree plot with Kaiser criterion line
+ * gg(data)
+ *   .aes({ x: 'component', y: 'eigenvalue' })
+ *   .geom(geom_scree({ show_kaiser: true }))
+ */
+import type { Geom } from '../types';
+export interface ScreeOptions {
+    /**
+     * Show cumulative variance line
+     * @default false
+     */
+    show_cumulative?: boolean;
+    /**
+     * Show Kaiser criterion line (eigenvalue = 1)
+     * @default false
+     */
+    show_kaiser?: boolean;
+    /**
+     * Show elbow point
+     * @default false
+     */
+    show_elbow?: boolean;
+    /**
+     * Show broken stick model line
+     * @default false
+     */
+    show_broken_stick?: boolean;
+    /**
+     * Connect points with lines
+     * @default true
+     */
+    connect_points?: boolean;
+    /**
+     * Show bars instead of/in addition to points
+     * @default false
+     */
+    show_bars?: boolean;
+    /**
+     * Point character
+     * @default '●'
+     */
+    point_char?: string;
+    /**
+     * Color for main line/points
+     * @default undefined (uses default palette)
+     */
+    color?: string;
+    /**
+     * Color for cumulative line
+     * @default '#ff0000'
+     */
+    cumulative_color?: string;
+    /**
+     * Color for Kaiser line
+     * @default '#888888'
+     */
+    kaiser_color?: string;
+    /**
+     * Y-axis as percentage (0-100) or proportion (0-1)
+     * @default 'percentage'
+     */
+    y_format?: 'percentage' | 'proportion' | 'eigenvalue';
+    /**
+     * Threshold line for variance explained (e.g., 0.8 for 80%)
+     * @default undefined
+     */
+    threshold?: number;
+    /**
+     * Color for threshold line
+     * @default '#00aa00'
+     */
+    threshold_color?: string;
+}
+/**
+ * Create a scree plot geometry
+ */
+export declare function geom_scree(options?: ScreeOptions): Geom;
+//# sourceMappingURL=scree.d.ts.map

package/dist/geoms/scree.d.ts.map

@@ -0,0 +1 @@
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package/dist/geoms/upset.d.ts

@@ -0,0 +1,63 @@
+/**
+ * UpSet Plot Geom
+ *
+ * Modern set intersection visualization, superior to Venn diagrams for >3 sets.
+ * Shows:
+ * - Matrix of set memberships (dots connected by lines)
+ * - Bar chart of intersection sizes
+ * - Optional set size bars
+ *
+ * Data format options:
+ * 1. Binary matrix: columns are sets, rows are elements (1 = member, 0 = not)
+ * 2. List format: 'sets' column with comma-separated set names
+ *
+ * @example
+ * // Binary matrix format
+ * const data = [
+ *   { A: 1, B: 1, C: 0 },
+ *   { A: 1, B: 0, C: 0 },
+ *   { A: 0, B: 1, C: 1 },
+ * ]
+ * gg(data).geom(geom_upset({ sets: ['A', 'B', 'C'] }))
+ *
+ * @example
+ * // List format
+ * const data = [
+ *   { element: 'gene1', sets: 'A,B' },
+ *   { element: 'gene2', sets: 'A' },
+ *   { element: 'gene3', sets: 'B,C' },
+ * ]
+ * gg(data).aes({ x: 'sets' }).geom(geom_upset())
+ */
+import type { Geom } from '../types';
+export interface UpsetOptions {
+    /** Set names for binary matrix format */
+    sets?: string[];
+    /** Minimum intersection size to display */
+    min_size?: number;
+    /** Maximum number of intersections to show */
+    max_intersections?: number;
+    /** Sort intersections by: 'size' (default), 'degree', 'sets' */
+    sort_by?: 'size' | 'degree' | 'sets';
+    /** Sort order */
+    sort_order?: 'desc' | 'asc';
+    /** Show set size bars on the left */
+    show_set_sizes?: boolean;
+    /** Character for filled dots in matrix */
+    dot_char?: string;
+    /** Character for empty positions in matrix */
+    empty_char?: string;
+    /** Character for connecting lines in matrix */
+    line_char?: string;
+    /** Bar character for intersection sizes */
+    bar_char?: string;
+    /** Color for dots and bars */
+    color?: string;
+    /** Show intersection degree (number of sets) */
+    show_degree?: boolean;
+}
+/**
+ * Create an UpSet plot geom for visualizing set intersections
+ */
+export declare function geom_upset(options?: UpsetOptions): Geom;
+//# sourceMappingURL=upset.d.ts.map

package/dist/geoms/upset.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"upset.d.ts","sourceRoot":"","sources":["../../src/geoms/upset.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8BG;AAEH,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,UAAU,CAAA;AAEpC,MAAM,WAAW,YAAY;IAC3B,yCAAyC;IACzC,IAAI,CAAC,EAAE,MAAM,EAAE,CAAA;IACf,2CAA2C;IAC3C,QAAQ,CAAC,EAAE,MAAM,CAAA;IACjB,8CAA8C;IAC9C,iBAAiB,CAAC,EAAE,MAAM,CAAA;IAC1B,gEAAgE;IAChE,OAAO,CAAC,EAAE,MAAM,GAAG,QAAQ,GAAG,MAAM,CAAA;IACpC,iBAAiB;IACjB,UAAU,CAAC,EAAE,MAAM,GAAG,KAAK,CAAA;IAC3B,qCAAqC;IACrC,cAAc,CAAC,EAAE,OAAO,CAAA;IACxB,0CAA0C;IAC1C,QAAQ,CAAC,EAAE,MAAM,CAAA;IACjB,8CAA8C;IAC9C,UAAU,CAAC,EAAE,MAAM,CAAA;IACnB,+CAA+C;IAC/C,SAAS,CAAC,EAAE,MAAM,CAAA;IAClB,2CAA2C;IAC3C,QAAQ,CAAC,EAAE,MAAM,CAAA;IACjB,8BAA8B;IAC9B,KAAK,CAAC,EAAE,MAAM,CAAA;IACd,gDAAgD;IAChD,WAAW,CAAC,EAAE,OAAO,CAAA;CACtB;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,OAAO,GAAE,YAAiB,GAAG,IAAI,CAoB3D"}

package/dist/index.d.ts

@@ -9,8 +9,8 @@ export type { AestheticMapping, Canvas, CanvasCell, ComputedPoint, Coord, DataRe
 export { TerminalCanvas, createCanvas, DEFAULT_FG, DEFAULT_BG } from './canvas';
 export { renderToCanvas, renderToString, calculateLayout, buildScaleContext, inferContinuousDomain, inferDiscreteDomain, } from './pipeline';
 export type { PlotLayout, ResolvedScale, ScaleContext } from './pipeline';
-export { geom_point, geom_line, geom_path, geom_hline, geom_vline, geom_bar, geom_col, geom_text, geom_label, geom_area, geom_ribbon, geom_histogram, geom_density, geom_boxplot, geom_segment, geom_curve, geom_smooth, geom_step, geom_rug, geom_violin, geom_tile, geom_raster, geom_bin2d, geom_contour, geom_contour_filled, geom_density_2d, geom_errorbar, geom_errorbarh, geom_crossbar, geom_linerange, geom_pointrange, geom_rect, geom_abline, geom_qq, geom_qq_line, geom_freqpoly, geom_ridgeline, geom_joy, geom_beeswarm, geom_quasirandom, geom_dumbbell, geom_lollipop, geom_waffle, geom_sparkline, geom_bullet, geom_braille, SPARK_BARS, SPARK_DOTS, BRAILLE_BASE, BRAILLE_DOTS, geom_calendar, geom_flame, geom_icicle, geom_corrmat, geom_sankey, geom_treemap, geom_volcano, } from './geoms';
-export type { PathOptions, RugOptions, SmoothOptions, StepOptions, ViolinOptions, TileOptions, Bin2dOptions, ContourOptions, ErrorbarOptions, RectOptions, AblineOptions, QQOptions, QQLineOptions, FreqpolyOptions, DensityOptions, RidgelineOptions, BeeswarmOptions, DumbbellOptions, LollipopOptions, WaffleOptions, SparklineOptions, BulletOptions, BrailleOptions, CalendarOptions, FlameOptions, CorrmatOptions, SankeyOptions, TreemapOptions, VolcanoOptions, } from './geoms';
+export { geom_point, geom_line, geom_path, geom_hline, geom_vline, geom_bar, geom_col, geom_text, geom_label, geom_area, geom_ribbon, geom_histogram, geom_density, geom_boxplot, geom_segment, geom_curve, geom_smooth, geom_step, geom_rug, geom_violin, geom_tile, geom_raster, geom_bin2d, geom_contour, geom_contour_filled, geom_density_2d, geom_errorbar, geom_errorbarh, geom_crossbar, geom_linerange, geom_pointrange, geom_rect, geom_abline, geom_qq, geom_freqpoly, geom_ridgeline, geom_joy, geom_beeswarm, geom_quasirandom, geom_dumbbell, geom_lollipop, geom_waffle, geom_sparkline, geom_bullet, geom_braille, SPARK_BARS, SPARK_DOTS, BRAILLE_BASE, BRAILLE_DOTS, geom_calendar, geom_flame, geom_icicle, geom_corrmat, geom_sankey, geom_treemap, geom_volcano, geom_ma, geom_manhattan, geom_heatmap, geom_biplot, geom_kaplan_meier, geom_forest, geom_roc, geom_bland_altman, geom_ecdf, geom_funnel, geom_control, geom_scree, geom_upset, geom_dendrogram, } from './geoms';
+export type { PathOptions, RugOptions, SmoothOptions, StepOptions, ViolinOptions, TileOptions, Bin2dOptions, ContourOptions, ErrorbarOptions, RectOptions, AblineOptions, QQOptions, FreqpolyOptions, DensityOptions, RidgelineOptions, BeeswarmOptions, DumbbellOptions, LollipopOptions, WaffleOptions, SparklineOptions, BulletOptions, BrailleOptions, CalendarOptions, FlameOptions, CorrmatOptions, SankeyOptions, TreemapOptions, VolcanoOptions, MAOptions, ManhattanOptions, HeatmapOptions, BiplotOptions, KaplanMeierOptions, ForestOptions, RocOptions, BlandAltmanOptions, ECDFOptions, FunnelOptions, ControlOptions, ScreeOptions, UpsetOptions, DendrogramOptions, } from './geoms';
 export { position_identity, position_dodge, position_stack, position_fill, position_jitter, applyPositionAdjustment, isStackPosition, isDodgePosition, getPositionType, } from './positions';
 export type { Position, AdjustedPoint, DodgeOptions, JitterOptions, StackOptions, FillOptions, } from './positions';
 export { stat_bin, stat_bin2d, stat_boxplot, stat_density, stat_smooth, stat_summary, stat_qq, stat_qq_line, computeBins, computeBins2d, computeBoxplotStats, computeDensity, computeSmooth, computeSummary, computeQQ, computeQQLine, stat_beeswarm, computeBeeswarm, } from './stats';

package/dist/index.d.ts.map

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