genome-spy-python 0.5.0__tar.gz → 0.6.0__tar.gz

{genome_spy_python-0.5.0 → genome_spy_python-0.6.0}/.gitignore

@@ -248,3 +248,6 @@ tools/__pycache__/
 scripts/*alphagenome*.py
 scripts/fetch_*_reference.py
 scripts/_fetch_reference.py
+
+# Local recording demos and working files
+/demos/

{genome_spy_python-0.5.0 → genome_spy_python-0.6.0}/CHANGELOG.md

@@ -5,6 +5,29 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.6.0] - 2026-10-01
+
+### Added
+
+- Add the prepared `airway_review` dataset for gene-review examples.
+
+### Changed
+
+- Upgrade GenomeSpy Core, controls, and Inspector to 1.0.0 and regenerate
+  the Python schema API, including configurable `displace2d` animation half-life.
+- Extend the sequence-editing notebook to support multi-base edits across the
+  displayed locus.
+- Improve interaction and PISA documentation, gallery expressions, and README
+  animations.
+
+### Fixed
+
+- Expose selection predicate classes through `gs` and support typed endpoint
+  projection setters, avoiding raw dictionaries in composed conditions.
+- Restrict sequence-logo and alignment-logo zoom to the position axis and share
+  one bottom alignment axis.
+- Render the ASCAT fitting example title as literal text.
+
 ## [0.5.0] - 2026-09-25
 
 ### Added
@@ -18,6 +41,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- Use browser-side `displace2d` label placement in the airway volcano and MA
+  gallery plots, with denser gene annotations and adaptive leader lines.
+
 - Reorganize the gallery into 13 categories, separating regulatory model
   interpretation, read alignments and RNA splicing, sequences and alignments,
   and interaction examples from the broader browser, annotation, and basic groups.

{genome_spy_python-0.5.0 → genome_spy_python-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: genome-spy-python
-Version: 0.5.0
+Version: 0.6.0
 Summary: genome-spy-python is a declarative genomics visualization library for Python, built on top of the genome-spy JSON specification.
 Project-URL: Homepage, https://github.com/genome-spy/genome-spy-python
 Project-URL: Documentation, https://genomespy.app/genome-spy-python/
@@ -102,59 +102,113 @@ See the [getting-started guide](docs/getting-started.md) for the first example.
 
 ## Examples
 
+A zoomable Manhattan plot using the bundled HapMap data (requires `pandas`):
+
 ```python
 import genome_spy as gs
+from genome_spy.datasets import load_dataset
 
 chart = (
-    gs.Chart(
-        [
-            {"x": 1, "y": 4, "group": "A"},
-            {"x": 2, "y": 3, "group": "B"},
-            {"x": 3, "y": 5, "group": "A"},
-        ]
-    )
-    .mark_point(size=80)
+    # Load data.
+    gs.Chart(load_dataset("hapmap_gwas"))
+    # Format chromosome names.
+    .transform_formula(expr="datum.CHR == 23 ? 'chrX' : 'chr' + datum.CHR", as_="chrom")
+    # Calculate −log10 p.
+    .transform_formula(expr="-log(datum.P) / log(10)", as_="neglogp")
+    # Draw variants.
+    .mark_point(size=12)
+    # Set positions and colors.
     .encode(
-        x="x:Q",
-        y="y:Q",
-        color="group:N",
+        x=gs.Locus("chrom", "BP").scale(assembly="hg18"),
+        y=gs.Y("neglogp:Q").title("−log10 p"),
+        color=gs.Color("CHR:N").scale(range=["#5b8fd6", "#8f98a3"]).legend(None),
     )
 )
-
 chart
 ```
 
-GenomeSpy also has locus-scaled axes for genomic coordinates. This small
-example renders intervals along a region of chromosome 1:
+![Manhattan plot zooming from the whole genome into an association peak](https://raw.githubusercontent.com/genome-spy/genome-spy-python/a6c724f48d94f86d8d0a8c3200549d7560a88a3c/docs/_static/readme-manhattan.webp)
+
+[Explore the full example and data provenance](https://genomespy.app/genome-spy-python/gallery/manhattan_plot.html).
+
+A sequence logo and aligned sequences with shared horizontal zoom:
 
 ```python
 import genome_spy as gs
 
-intervals = [
-    {"chrom": "chr1", "start": 100, "end": 220, "name": "gene A"},
-    {"chrom": "chr1", "start": 280, "end": 420, "name": "gene B"},
-]
-
+logo = (
+    gs.Chart()
+    # Count bases at each position.
+    .transform_aggregate(groupby=["pos", "sequence"])
+    # Handle gaps.
+    .transform_formula(expr="datum.sequence == '-' ? null : datum.sequence", as_="base")
+    # Stack bases by information content.
+    .transform_stack(
+        field="count",
+        groupby=["pos"],
+        offset="information",
+        baseField="base",
+        as_=["y0", "y1"],
+    )
+    # Draw logo letters.
+    .mark_text(logoLetters=True, fitToBand=True, fontWeight="bold")
+    # Set stack bounds.
+    .encode(
+        y=gs.Y("y0:Q").scale(domain=[0, 2], zoom=False).title("Bits"),
+        y2="y1:Q",
+        text="base:N",
+    )
+    .properties(height=100)
+)
+# Create sequence rows.
+rows = gs.Chart().encode(y=gs.Y("identifier:N").scale(zoom=False).axis(None))
+# Add base labels.
+letters = rows.mark_text(size=11, fitToBand=True, opacity=0.7).encode(
+    text="sequence:N", color=gs.value("black")
+)
+# Layer tiles and labels.
+sequences = (rows.mark_rect() + letters).properties(
+    height=gs.step(16), viewportHeight=160
+)
 chart = (
-    gs.Chart(intervals)
-    .mark_rect()
+    # Combine panels.
+    (logo & sequences)
+    # Load data.
+    .properties(
+        data=gs.Data(
+            url="https://data.genomespy.app/sample-data/16SRNA_Deino_87seq.aln",
+            format=gs.data_format(type="fasta"),
+        )
+    )
+    # Split sequences into bases.
+    .transform_flatten_sequence()
+    # Set positions and colors.
     .encode(
-        x=gs.Locus("chrom", "start"),
-        x2="end:Q",
-        y="name:N",
-        color="name:N",
+        x=gs.X("pos:I").scale(domain=[190, 310], zoom=True).title(None),
+        color=gs.Color("sequence:N")
+        .scale(
+            domain=list("ACTGN-"),
+            range=["#4FBF45", "#4D96E8", "#E85F78", "#E8B322", "#BDBDBD", "#f5f5f5"],
+        )
+        .legend(None),
     )
+    # Share zoom and colors.
+    .resolve_scale(x="shared", color="shared")
+    .resolve_axis(x="shared")
 )
-
 chart
 ```
 
+![Sequence logo and aligned sequences zooming across multiple regions](https://raw.githubusercontent.com/genome-spy/genome-spy-python/main/docs/_static/readme-sequence-logo.webp?v=4cd9f86a0d31)
+
 Charts can be serialized to a portable GenomeSpy specification or standalone
 HTML:
 
 ```python
+# Export JSON.
 chart.to_json()
-chart.save("intervals.html")
+# Save HTML.
+chart.save("chart.html")
 ```
 
 ### Update data without recreating the chart
@@ -165,12 +219,15 @@ existing GenomeSpy instance, so view state such as zoom is preserved.
 
 ```python
 chart = (
+    # Create an empty chart.
     gs.Chart(data={"name": "table"}, datasets={"table": []})
     .mark_point()
     .encode(x="x:Q", y="y:Q")
 )
+# Show widget.
 view = chart.widget()
 
+# Update data.
 view.set_dataset("table", updated_dataframe)
 ```
 

{genome_spy_python-0.5.0 → genome_spy_python-0.6.0}/README.md

@@ -63,59 +63,113 @@ See the [getting-started guide](docs/getting-started.md) for the first example.
 
 ## Examples
 
+A zoomable Manhattan plot using the bundled HapMap data (requires `pandas`):
+
 ```python
 import genome_spy as gs
+from genome_spy.datasets import load_dataset
 
 chart = (
-    gs.Chart(
-        [
-            {"x": 1, "y": 4, "group": "A"},
-            {"x": 2, "y": 3, "group": "B"},
-            {"x": 3, "y": 5, "group": "A"},
-        ]
-    )
-    .mark_point(size=80)
+    # Load data.
+    gs.Chart(load_dataset("hapmap_gwas"))
+    # Format chromosome names.
+    .transform_formula(expr="datum.CHR == 23 ? 'chrX' : 'chr' + datum.CHR", as_="chrom")
+    # Calculate −log10 p.
+    .transform_formula(expr="-log(datum.P) / log(10)", as_="neglogp")
+    # Draw variants.
+    .mark_point(size=12)
+    # Set positions and colors.
     .encode(
-        x="x:Q",
-        y="y:Q",
-        color="group:N",
+        x=gs.Locus("chrom", "BP").scale(assembly="hg18"),
+        y=gs.Y("neglogp:Q").title("−log10 p"),
+        color=gs.Color("CHR:N").scale(range=["#5b8fd6", "#8f98a3"]).legend(None),
     )
 )
-
 chart
 ```
 
-GenomeSpy also has locus-scaled axes for genomic coordinates. This small
-example renders intervals along a region of chromosome 1:
+![Manhattan plot zooming from the whole genome into an association peak](https://raw.githubusercontent.com/genome-spy/genome-spy-python/a6c724f48d94f86d8d0a8c3200549d7560a88a3c/docs/_static/readme-manhattan.webp)
+
+[Explore the full example and data provenance](https://genomespy.app/genome-spy-python/gallery/manhattan_plot.html).
+
+A sequence logo and aligned sequences with shared horizontal zoom:
 
 ```python
 import genome_spy as gs
 
-intervals = [
-    {"chrom": "chr1", "start": 100, "end": 220, "name": "gene A"},
-    {"chrom": "chr1", "start": 280, "end": 420, "name": "gene B"},
-]
-
+logo = (
+    gs.Chart()
+    # Count bases at each position.
+    .transform_aggregate(groupby=["pos", "sequence"])
+    # Handle gaps.
+    .transform_formula(expr="datum.sequence == '-' ? null : datum.sequence", as_="base")
+    # Stack bases by information content.
+    .transform_stack(
+        field="count",
+        groupby=["pos"],
+        offset="information",
+        baseField="base",
+        as_=["y0", "y1"],
+    )
+    # Draw logo letters.
+    .mark_text(logoLetters=True, fitToBand=True, fontWeight="bold")
+    # Set stack bounds.
+    .encode(
+        y=gs.Y("y0:Q").scale(domain=[0, 2], zoom=False).title("Bits"),
+        y2="y1:Q",
+        text="base:N",
+    )
+    .properties(height=100)
+)
+# Create sequence rows.
+rows = gs.Chart().encode(y=gs.Y("identifier:N").scale(zoom=False).axis(None))
+# Add base labels.
+letters = rows.mark_text(size=11, fitToBand=True, opacity=0.7).encode(
+    text="sequence:N", color=gs.value("black")
+)
+# Layer tiles and labels.
+sequences = (rows.mark_rect() + letters).properties(
+    height=gs.step(16), viewportHeight=160
+)
 chart = (
-    gs.Chart(intervals)
-    .mark_rect()
+    # Combine panels.
+    (logo & sequences)
+    # Load data.
+    .properties(
+        data=gs.Data(
+            url="https://data.genomespy.app/sample-data/16SRNA_Deino_87seq.aln",
+            format=gs.data_format(type="fasta"),
+        )
+    )
+    # Split sequences into bases.
+    .transform_flatten_sequence()
+    # Set positions and colors.
     .encode(
-        x=gs.Locus("chrom", "start"),
-        x2="end:Q",
-        y="name:N",
-        color="name:N",
+        x=gs.X("pos:I").scale(domain=[190, 310], zoom=True).title(None),
+        color=gs.Color("sequence:N")
+        .scale(
+            domain=list("ACTGN-"),
+            range=["#4FBF45", "#4D96E8", "#E85F78", "#E8B322", "#BDBDBD", "#f5f5f5"],
+        )
+        .legend(None),
     )
+    # Share zoom and colors.
+    .resolve_scale(x="shared", color="shared")
+    .resolve_axis(x="shared")
 )
-
 chart
 ```
 
+![Sequence logo and aligned sequences zooming across multiple regions](https://raw.githubusercontent.com/genome-spy/genome-spy-python/main/docs/_static/readme-sequence-logo.webp?v=4cd9f86a0d31)
+
 Charts can be serialized to a portable GenomeSpy specification or standalone
 HTML:
 
 ```python
+# Export JSON.
 chart.to_json()
-chart.save("intervals.html")
+# Save HTML.
+chart.save("chart.html")
 ```
 
 ### Update data without recreating the chart
@@ -126,12 +180,15 @@ existing GenomeSpy instance, so view state such as zoom is preserved.
 
 ```python
 chart = (
+    # Create an empty chart.
     gs.Chart(data={"name": "table"}, datasets={"table": []})
     .mark_point()
     .encode(x="x:Q", y="y:Q")
 )
+# Show widget.
 view = chart.widget()
 
+# Update data.
 view.set_dataset("table", updated_dataframe)
 ```
 

{genome_spy_python-0.5.0 → genome_spy_python-0.6.0}/THIRD_PARTY_NOTICES.md

@@ -14,6 +14,10 @@ browser files are generated from the pinned `@genome-spy/core` and
 `@genome-spy/inspector` npm releases and include their bundled open-source
 runtime dependencies.
 
+The workflow menu and dialog styles in `docs/_static/workflows.css` adapt
+GenomeSpy App's `_generic.scss`, `baseDialog.js`, and `componentStyles.js`
+under the same MIT license.
+
 The Core browser bundle embeds the Lato font bitmap and metrics, copyright
 2010–2014 tyPoland Lukasz Dziedzic, with Reserved Font Name "Lato", under the
 SIL Open Font License 1.1. Its full upstream notice is retained in
@@ -169,3 +173,12 @@ The adapted areas are:
   `tools/generate_schema_wrapper.py`;
 - the multifeature penguins and cars strip-plot cases in `tests/test_chart.py`,
   adapted from Altair's example suite and mark documentation.
+
+## Prepared airway review table
+
+`airway_review.json.gz` uses the same Bioconnector workshop tables and paired
+log-count t-tests as the gallery volcano example. Source attribution and
+CC BY-NC-SA 4.0 terms are listed under Airway data above. Added fields contain
+gallery statistics, display values, sample counts, and host aliases;
+`tools/prepare_airway_review.py` reproduces the transformation. Source checksums
+are retained in the bundle. No PyDESeq2 analysis is used.

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{genome_spy_python-0.5.0 → genome_spy_python-0.6.0}/docs/_static/workflows.css

@@ -11,18 +11,20 @@
 .gs-workflow input, .gs-workflow button {
   font: inherit;
   padding: 0.45rem 0.65rem;
-  border: 1px solid var(--color-foreground-border);
+  border: 1px solid var(--color-foreground-border, #d6dce5);
   border-radius: 4px;
-  color: var(--color-foreground-primary);
-  background: var(--color-background-secondary);
+  color: var(--color-foreground-primary, #172637);
+  background: var(--color-background-secondary, #ffffff);
 }
 .gs-workflow button:not(:disabled) { cursor: pointer; }
 .gs-workflow button:disabled { opacity: 0.5; }
+.gs-workflow [data-draft] { flex-basis: 100%; margin: 0; }
+.gs-workflow-table button { margin: 0.15rem; }
 .gs-workflow-table { overflow: auto; max-height: 18rem; }
 .gs-workflow-table table { width: 100%; font-size: 0.85rem; border-collapse: collapse; }
 .gs-workflow-table th, .gs-workflow-table td {
   padding: 0.4rem 0.5rem;
-  border-bottom: 1px solid var(--color-foreground-border);
+  border-bottom: 1px solid var(--color-foreground-border, #d6dce5);
   text-align: left;
   overflow-wrap: anywhere;
 }

{genome_spy_python-0.5.0 → genome_spy_python-0.6.0}/docs/api.md

@@ -144,12 +144,17 @@ Schema-backed configuration objects accepted by charts, channels, and helpers.
    GenomeAxis
    HandledTooltip
    Legend
+   NamedSelectionPredicateRef
    Paddings
    Parameter
+   ParameterPredicate
    Parse
    RulerMarkConfig
    Scale
    SelectionDomainRef
+   SelectionPredicateDefinition
+   SelectionPredicateOperand
+   SelectionUnionTest
    SizeDef
    Step
    Title

{genome_spy_python-0.5.0 → genome_spy_python-0.6.0}/docs/datasets.md

@@ -27,6 +27,7 @@ for JSON files. Pass `as_format="text"` to get the raw file contents instead.
 
 | Dataset | Contents |
 | --- | --- |
+| `airway_review` | Gallery airway statistics and sample counts for downstream gene review |
 | `airway_metadata` | Sample table for the airway RNA-seq experiment |
 | `airway_scaledcounts` | Rounded, length-scaled gene counts for the same eight samples |
 | `hapmap_gwas` | HapMap coordinates with simulated p-values and effect sizes |

{genome_spy_python-0.5.0 → genome_spy_python-0.6.0}/docs/examples/airway_ma_plot.py

@@ -27,7 +27,7 @@ MAX_GENES = 12_000
 ZOOM_LEVEL = gs.Expression("zoomLevel")
 POINT_SIZE = gs.expr(gs.expr.min(14 * gs.expr.pow(ZOOM_LEVEL, 0.75), 64))
 
-# Load gene results with fold changes, p-values, and label positions ready to use.
+# Load gene results with fold changes, p-values, and selected gene labels.
 data, domains = airway_differential_expression(
     min_base_mean=MIN_BASE_MEAN,
     max_genes=MAX_GENES,
@@ -114,74 +114,87 @@ ma_fc_rules = (
     )
 )
 
-# Connect the selected gene labels to their points.
+# Share the displaced layout between labels and their shortened leader lines.
 ma_callout_lines = (
     gs.Chart()
-    .transform_collect()
-    .transform_filter(gs.datum.ma_label)
     .mark_rule(color="#3f4750", size=1, tooltip=None)
     .encode(
-        x=gs.X("log10_base_mean:Q")
-        .scale(domain=domains["ma_x"], zoom=True)
-        .title("log10 mean count"),
-        xOffset=gs.XOffset("ma_x_offset:Q").scale(None),
-        y=gs.Y("log2fc:Q")
-        .scale(reverse=False, domain=domains["ma_y"], zoom=True)
-        .title("log2 fold change"),
-        yOffset=gs.YOffset("ma_y_offset:Q").scale(None),
         x2=gs.X2("log10_base_mean"),
         y2=gs.Y2("log2fc"),
+        xOffset=gs.XOffset("leader_dx:Q").scale(None),
+        yOffset=gs.YOffset("leader_dy:Q").scale(None),
     )
     .properties(name="ma-callout-lines")
 )
 
-
-def ma_callout_label(*, side: str, name: str) -> gs.Chart:
-    """Build one label layer just beyond its shortened leader line."""
-    return (
-        gs.Chart()
-        .transform_collect()
-        .transform_filter(gs.datum.ma_label & (gs.datum.ma_label_side == side))
-        .mark_text(
-            align="right" if side == "left" else "left",
-            baseline="middle",
-            dx=-4 if side == "left" else 4,
-            dy=0,
-            fontWeight="bold",
-            color="#20262d",
-            tooltip=None,
-        )
-        .encode(
-            x=gs.X("log10_base_mean:Q")
-            .scale(domain=domains["ma_x"], zoom=True)
-            .title("log10 mean count"),
-            xOffset=gs.XOffset("ma_x_offset:Q").scale(None),
-            y=gs.Y("log2fc:Q")
-            .scale(reverse=False, domain=domains["ma_y"], zoom=True)
-            .title("log2 fold change"),
-            yOffset=gs.YOffset("ma_y_offset:Q").scale(None),
-            text=gs.Text("ma_label:N"),
-        )
-        .properties(name=name)
+ma_callout_labels = (
+    gs.Chart()
+    .mark_text(
+        align="center",
+        baseline="middle",
+        size=14,
+        fontWeight="bold",
+        color="#20262d",
+        tooltip=None,
     )
+    .encode(
+        text=gs.Text("ma_label:N"),
+        xOffset=gs.XOffset("label_dx:Q").scale(None),
+        yOffset=gs.YOffset("label_dy:Q").scale(None),
+    )
+    .properties(name="ma-labels")
+)
 
-
-# Place labels on either side, leaving a small gap after each line.
-ma_callout_labels = [
-    ma_callout_label(
-        side=side,
-        name=f"ma-label-{side}",
+ma_annotations = (
+    (ma_callout_lines + ma_callout_labels)
+    .transform_filter(gs.datum.ma_label)
+    .transform_measure_text(
+        field="ma_label", fontSize=14, fontWeight="bold", as_="label_width"
     )
-    for side in ("left", "right")
-]
+    .transform_formula(expr=gs.datum.label_width + 4, as_="label_width")
+    .transform_collect()
+    .transform_filter(
+        gs.expr.inrange(gs.datum.log10_base_mean, gs.expr.domain("x"))
+        & gs.expr.inrange(gs.datum.log2fc, gs.expr.domain("y"))
+    )
+    # Tight collision boxes reduce unnecessary separation during zooming.
+    .transform_displace2d(
+        key="ensgene",
+        x="log10_base_mean",
+        y="log2fc",
+        width="label_width",
+        height=16,
+        anchorWidth=8,
+        anchorHeight=8,
+        as_=["label_dx", "label_dy"],
+    )
+    # Stop each leader at the padded label box instead of crossing the text.
+    .transform_formula(
+        expr=gs.expr.max(
+            0,
+            1
+            - gs.expr.min(
+                gs.datum.label_width / 2 / gs.expr.max(abs(gs.datum.label_dx), 1e-6),
+                8 / gs.expr.max(abs(gs.datum.label_dy), 1e-6),
+            ),
+        ),
+        as_="leader_scale",
+    )
+    .transform_formula(expr=gs.datum.label_dx * gs.datum.leader_scale, as_="leader_dx")
+    .transform_formula(expr=gs.datum.label_dy * gs.datum.leader_scale, as_="leader_dy")
+    .encode(
+        x=gs.X("log10_base_mean:Q").title("log10 mean count"),
+        y=gs.Y("log2fc:Q").title("log2 fold change"),
+    )
+    .properties(name="ma-annotations")
+)
 
 # Put the points, guides, and labels together, then attach the sliders.
 chart = (
     gs.layer(
         ma_fc_rules,
         ma_points,
-        ma_callout_lines,
-        *ma_callout_labels,
+        ma_annotations,
     )
     .properties(
         data=data,