genome-spy-python 0.1.0__py3-none-any.whl

genome_spy/datasets/data/tcga_laml_annot.tsv

@@ -0,0 +1,201 @@
+Tumor_Sample_Barcode	FAB_classification	days_to_last_followup	Overall_Survival_Status
+TCGA-AB-2802	M4	365	1
+TCGA-AB-2803	M3	792	1
+TCGA-AB-2804	M3	2557	0
+TCGA-AB-2805	M0	577	1
+TCGA-AB-2806	M1	945	1
+TCGA-AB-2807	M1	181	1
+TCGA-AB-2808	M2	2861	0
+TCGA-AB-2809	M3	62	1
+TCGA-AB-2810	M2	31	1
+TCGA-AB-2811	M4	243	1
+TCGA-AB-2812	M2	366	1
+TCGA-AB-2813	M4	31	1
+TCGA-AB-2814	M0	792	1
+TCGA-AB-2815	M4	822	1
+TCGA-AB-2816	M4	245	1
+TCGA-AB-2817	M2	273	1
+TCGA-AB-2818	M2	303	1
+TCGA-AB-2819	M2	2496	0
+TCGA-AB-2820	M0	0	1
+TCGA-AB-2821	M1	822	1
+TCGA-AB-2822	M0	973	1
+TCGA-AB-2823	M3	0	1
+TCGA-AB-2824	M5	30	1
+TCGA-AB-2825	M5	212	1
+TCGA-AB-2826	M4	731	1
+TCGA-AB-2827	M2	273	1
+TCGA-AB-2828	M4	2284	0
+TCGA-AB-2829	M6	273	1
+TCGA-AB-2830	M4	275	1
+TCGA-AB-2831	M0	640	1
+TCGA-AB-2832	M5	365	1
+TCGA-AB-2833	M4	456	1
+TCGA-AB-2834	M4	245	1
+TCGA-AB-2835	M5	1673	0
+TCGA-AB-2836	M4	518	1
+TCGA-AB-2837	M5	0	1
+TCGA-AB-2838	M2	365	1
+TCGA-AB-2839	M2	486	1
+TCGA-AB-2840	M3	28	1
+TCGA-AB-2841	M3	1401	1
+TCGA-AB-2842	M4	0	1
+TCGA-AB-2843	M6	215	1
+TCGA-AB-2844	M2	122	1
+TCGA-AB-2845	M2	304	1
+TCGA-AB-2846	M4	1402	1
+TCGA-AB-2847	M1	608	1
+TCGA-AB-2848	M4	455	1
+TCGA-AB-2849	M0	2220	0
+TCGA-AB-2850	M2	61	1
+TCGA-AB-2851	M5	242	1
+TCGA-AB-2853	M1	89	1
+TCGA-AB-2854	M4	366	1
+TCGA-AB-2855	M1	212	1
+TCGA-AB-2856	M4	150	1
+TCGA-AB-2857	M6	306	1
+TCGA-AB-2858	M2	577	1
+TCGA-AB-2859	M2	304	1
+TCGA-AB-2860	M7	427	1
+TCGA-AB-2861	M5	0	1
+TCGA-AB-2862	M3	1430	0
+TCGA-AB-2863	M1	31	1
+TCGA-AB-2864	M1	577	1
+TCGA-AB-2865	M1	61	1
+TCGA-AB-2866	M1	153	1
+TCGA-AB-2867	M2	184	1
+TCGA-AB-2868	M7	151	1
+TCGA-AB-2869	M2	243	0
+TCGA-AB-2870	M1	153	1
+TCGA-AB-2871	M1	153	0
+TCGA-AB-2872	M3	638	0
+TCGA-AB-2873	M5	273	0
+TCGA-AB-2874	M2	396	0
+TCGA-AB-2875	M2	212	0
+TCGA-AB-2876	M2	1219	0
+TCGA-AB-2877	M1	638	0
+TCGA-AB-2878	M2	365	1
+TCGA-AB-2879	M1	245	0
+TCGA-AB-2880	M1	424	1
+TCGA-AB-2881	M1	393	0
+TCGA-AB-2882	M2	365	1
+TCGA-AB-2883	M5	730	0
+TCGA-AB-2884	M1	731	1
+TCGA-AB-2885	M0	214	1
+TCGA-AB-2886	M2	181	0
+TCGA-AB-2887	M1	-Inf	1
+TCGA-AB-2888	M4	334	0
+TCGA-AB-2889	M4	304	0
+TCGA-AB-2890	M0	0	1
+TCGA-AB-2891	M1	-Inf	1
+TCGA-AB-2892	M4	943	0
+TCGA-AB-2893	M5	212	1
+TCGA-AB-2894	M5	181	1
+TCGA-AB-2895	M1	153	1
+TCGA-AB-2896	M5	214	1
+TCGA-AB-2897	M3	243	0
+TCGA-AB-2898	M1	393	0
+TCGA-AB-2899	M4	671	1
+TCGA-AB-2900	M1	184	1
+TCGA-AB-2901	M2	59	0
+TCGA-AB-2903	M1	0	1
+TCGA-AB-2904	M0	517	1
+TCGA-AB-2905	M3	1611	0
+TCGA-AB-2906	M3	577	0
+TCGA-AB-2907	M0	-Inf	1
+TCGA-AB-2908	M2	31	1
+TCGA-AB-2909	M0	30	0
+TCGA-AB-2910	M5	0	1
+TCGA-AB-2911	M4	1186	0
+TCGA-AB-2912	M4	274	1
+TCGA-AB-2913	M0	1216	0
+TCGA-AB-2914	M2	792	0
+TCGA-AB-2915	M2	0	1
+TCGA-AB-2916	M4	882	0
+TCGA-AB-2917	M0	1216	0
+TCGA-AB-2918	M1	-Inf	1
+TCGA-AB-2919	M1	61	0
+TCGA-AB-2920	M2	366	1
+TCGA-AB-2921	M4	-Inf	1
+TCGA-AB-2922	M0	0	1
+TCGA-AB-2923	M4	31	1
+TCGA-AB-2924	M4	90	0
+TCGA-AB-2925	M5	243	1
+TCGA-AB-2926	M1	457	1
+TCGA-AB-2927	M1	90	1
+TCGA-AB-2928	M1	59	1
+TCGA-AB-2929	M0	123	1
+TCGA-AB-2930	M2	-Inf	1
+TCGA-AB-2931	M2	0	1
+TCGA-AB-2932	M5	0	0
+TCGA-AB-2933	M4	122	1
+TCGA-AB-2934	M1	28	0
+TCGA-AB-2935	M4	61	1
+TCGA-AB-2936	M0	59	0
+TCGA-AB-2937	M1	215	1
+TCGA-AB-2938	M7	304	1
+TCGA-AB-2939	M1	455	0
+TCGA-AB-2940	M2	-Inf	1
+TCGA-AB-2941	NA	0	1
+TCGA-AB-2942	M4	641	0
+TCGA-AB-2943	M1	-Inf	1
+TCGA-AB-2944	M0	-Inf	1
+TCGA-AB-2945	M4	243	1
+TCGA-AB-2946	M2	-Inf	0
+TCGA-AB-2947	M4	31	0
+TCGA-AB-2948	M4	580	1
+TCGA-AB-2949	M0	699	0
+TCGA-AB-2950	M2	306	0
+TCGA-AB-2952	M1	31	1
+TCGA-AB-2954	M4	1492	0
+TCGA-AB-2955	M2	489	1
+TCGA-AB-2956	M5	183	1
+TCGA-AB-2957	M4	609	0
+TCGA-AB-2959	M0	489	1
+TCGA-AB-2963	M1	1642	1
+TCGA-AB-2964	M1	1277	0
+TCGA-AB-2965	M4	335	1
+TCGA-AB-2966	M2	854	1
+TCGA-AB-2967	M4	1035	0
+TCGA-AB-2968	M4	458	1
+TCGA-AB-2969	M5	1127	0
+TCGA-AB-2970	M4	305	1
+TCGA-AB-2971	M4	792	1
+TCGA-AB-2972	M2	30	1
+TCGA-AB-2973	M4	609	1
+TCGA-AB-2974	M5	92	1
+TCGA-AB-2975	M2	-Inf	1
+TCGA-AB-2976	M1	915	1
+TCGA-AB-2977	M2	31	1
+TCGA-AB-2978	M2	699	0
+TCGA-AB-2979	M1	671	0
+TCGA-AB-2980	M3	699	0
+TCGA-AB-2981	M5	487	0
+TCGA-AB-2982	M3	150	0
+TCGA-AB-2983	M0	335	1
+TCGA-AB-2984	M1	1157	0
+TCGA-AB-2985	M5	273	1
+TCGA-AB-2986	M2	212	1
+TCGA-AB-2987	M5	184	1
+TCGA-AB-2988	M1	30	1
+TCGA-AB-2989	M2	365	1
+TCGA-AB-2990	M1	457	0
+TCGA-AB-2991	M3	1826	0
+TCGA-AB-2992	M1	1706	1
+TCGA-AB-2993	M4	761	1
+TCGA-AB-2994	M3	1798	0
+TCGA-AB-2995	M2	1551	0
+TCGA-AB-2996	M2	1581	0
+TCGA-AB-2997	M3	-Inf	1
+TCGA-AB-2998	M3	31	1
+TCGA-AB-2999	M3	1735	0
+TCGA-AB-3000	M2	1249	0
+TCGA-AB-3001	M3	1581	0
+TCGA-AB-3002	M2	1431	1
+TCGA-AB-3005	M5	2100	0
+TCGA-AB-3006	M1	485	1
+TCGA-AB-3007	M3	1581	0
+TCGA-AB-3008	M1	822	1
+TCGA-AB-3009	M4	577	1
+TCGA-AB-3011	M1	1885	0
+TCGA-AB-3012	M3	1887	0

genome_spy/helpers.py

@@ -0,0 +1,185 @@
+"""Small ergonomic helpers for common GenomeSpy schema objects.
+
+These mirror Altair's pattern of exposing a small handwritten authoring layer
+on top of generated schema wrappers, so docs and examples can avoid repetitive
+raw dictionaries.
+
+The module intentionally contains two kinds of helpers:
+
+- tiny readability-first constructors such as ``expr(...)`` and ``step(...)``,
+- generated schema-object constructors and the two mapping-shaped helpers
+  whose keys are intentionally open-ended.
+"""
+
+from __future__ import annotations
+
+from typing import Any, Unpack, cast, overload
+
+from genome_spy._conditions import when
+from genome_spy._parameters import Parameter
+from genome_spy.schema._kwds import AxesKwds, ScalesKwds
+from genome_spy.schema._typing import ParseValue_T
+from genome_spy.schema.core import (
+    ConditionalParameterValueDefNumberExprRef,
+    ConditionalParameterValueDefStringNullExprRef,
+    ExprRef,
+    Parse,
+    Step,
+)
+from genome_spy.schema.expressions import expr
+from genome_spy.schema.ergonomics import (
+    config,
+    data_format,
+    dynamic_opacity,
+    title,
+    view,
+    view_config,
+)
+
+# BEGIN GENERATED INTERACTION IMPORTS
+from genome_spy.schema.ergonomics import (
+    binding,
+    binding_checkbox,
+    binding_radio,
+    binding_range,
+    binding_select,
+    param,
+    ruler,
+    selection_interval,
+    selection_point,
+)
+
+# END GENERATED INTERACTION IMPORTS
+from genome_spy.schemapi import Undefined, UndefinedType, normalize_schema_value
+
+
+def _normalized_mapping_payload(**kwargs: Any) -> dict[str, Any]:
+    """Return schema-normalized key/value pairs for mapping-style helpers."""
+    return {
+        key: normalize_schema_value(value, validate=False)
+        for key, value in kwargs.items()
+    }
+
+
+__all__ = [
+    "axes",
+    "config",
+    "condition",
+    "data_format",
+    "dynamic_opacity",
+    "expr",
+    "parse",
+    "scales",
+    "step",
+    "title",
+    "view",
+    "view_config",
+    "when",
+    # BEGIN GENERATED INTERACTION EXPORTS
+    "binding",
+    "binding_checkbox",
+    "binding_radio",
+    "binding_range",
+    "binding_select",
+    "param",
+    "ruler",
+    "selection_interval",
+    "selection_point",
+    # END GENERATED INTERACTION EXPORTS
+]
+
+
+def axes(**kwargs: Unpack[AxesKwds]) -> AxesKwds:
+    """Create top-level shared axis configuration.
+
+    Args:
+        **kwargs: Axis configuration keyed by channel name.
+
+    Returns:
+        A normalized typed axis mapping.
+
+    Example:
+        >>> axes(x=GenomeAxis(orient="top"))
+        {'x': {'orient': 'top'}}
+    """
+    return cast(AxesKwds, _normalized_mapping_payload(**kwargs))
+
+
+@overload
+def condition(
+    param: str | Parameter,
+    value: float | ExprRef,
+    /,
+    *,
+    empty: bool | UndefinedType = Undefined,
+) -> ConditionalParameterValueDefNumberExprRef: ...
+
+
+@overload
+def condition(
+    param: str | Parameter,
+    value: str | None,
+    /,
+    *,
+    empty: bool | UndefinedType = Undefined,
+) -> ConditionalParameterValueDefStringNullExprRef: ...
+
+
+def condition(
+    param: str | Parameter,
+    value: float | str | None | ExprRef,
+    /,
+    *,
+    empty: bool | UndefinedType = Undefined,
+) -> (
+    ConditionalParameterValueDefNumberExprRef
+    | ConditionalParameterValueDefStringNullExprRef
+):
+    """Create a parameter predicate for a conditional encoding value.
+
+    Args:
+        param: Name of the parameter to test.
+        value: Visual value applied when the parameter predicate matches.
+        empty: Whether an empty parameter selection matches.
+
+    Returns:
+        A schema-backed conditional value definition.
+
+    Example:
+        >>> condition("hover", 1, empty=False).to_dict()
+        {'empty': False, 'param': 'hover', 'value': 1}
+    """
+    if isinstance(param, Parameter):
+        if not param.is_selection:
+            raise TypeError("condition() requires a selection parameter.")
+        parameter_name = param.name
+        resolved_empty = param.empty if empty is Undefined else empty
+    else:
+        parameter_name = param
+        resolved_empty = True if empty is Undefined else empty
+    if isinstance(value, str) or value is None:
+        return ConditionalParameterValueDefStringNullExprRef(
+            param=parameter_name, empty=resolved_empty, value=value
+        )
+    return ConditionalParameterValueDefNumberExprRef(
+        param=parameter_name, empty=resolved_empty, value=value
+    )
+
+
+def step(value: float, /) -> Step:
+    """Create a step-sized dimension wrapper."""
+    return Step(step=value)
+
+
+def parse(**kwargs: ParseValue_T) -> Parse:
+    """Create a parse mapping for a data format."""
+    return Parse(**kwargs)
+
+
+def scales(**kwargs: Unpack[ScalesKwds]) -> ScalesKwds:
+    """Create top-level shared scale configuration.
+
+    This remains a small handwritten helper because the schema models shared
+    scales as a typed mapping rather than a dedicated wrapper object.
+    """
+    return cast(ScalesKwds, _normalized_mapping_payload(**kwargs))

genome_spy/jupyter.py

@@ -0,0 +1,5 @@
+"""Notebook widget integration for GenomeSpy charts."""
+
+from genome_spy._widget import JupyterChart
+
+__all__ = ["JupyterChart"]