genome-spy-python 0.2.0__tar.gz → 0.3.0__tar.gz

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/CHANGELOG.md

@@ -5,6 +5,20 @@ 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).
 
+## [0.3.0] - 2026-09-09
+
+### Changed
+
+- **Dataset format change:** `p53_sequence_comparison` now contains 34 protein
+  sequences aligned with MAFFT L-INS-i, replacing the unaligned JSON tables.
+  Load the aligned FASTA with
+  `load_dataset("p53_sequence_comparison", as_format="text")`; code expecting
+  the previous mapping of prepared tables must be updated.
+- Updated the P53 gallery example to show the aligned sequences and calculate
+  conservation, gap-free fractions, and sequence logos in GenomeSpy.
+- Made the brush notebook build progressively from a simple p-value chart to
+  linked tracks, and added an effect-size zero baseline in the notebook and gallery.
+
 ## [0.2.0] - 2026-09-09
 
 ### Added
@@ -45,5 +59,6 @@ First public alpha release, targeting GenomeSpy Core 0.87.0.
 - Packaged example datasets, documentation, tutorials, and an interactive
   visualization gallery.
 
+[0.3.0]: https://github.com/genome-spy/genome-spy-python/compare/v0.2.0...v0.3.0
 [0.2.0]: https://github.com/genome-spy/genome-spy-python/compare/v0.1.0...v0.2.0
 [0.1.0]: https://github.com/genome-spy/genome-spy-python/releases/tag/v0.1.0

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: genome-spy-python
-Version: 0.2.0
+Version: 0.3.0
 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/

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/THIRD_PARTY_NOTICES.md

@@ -4,12 +4,11 @@
 
 `tcga_laml_combined_oncoplot.json.gz` contains prepared TCGA LAML tables from
 maftools revision `015a4cf8c69ba89a55a3fdcea911421509e9a198` (Anand Mayakonda,
-MIT). `p53_sequence_comparison.json.gz` contains p53 sequences and derived
-display tables from Plotly's datasets revision
-`0c447c47b757ad74edecab31f0d72f849d2e67c2` (Plotly Technologies Inc., MIT).
-Source file hashes are retained in the packaged data. The corresponding gallery
-pages describe processing. Copyright notices and terms are included in
-`LICENSES/GALLERY-DATA-MIT.txt`.
+MIT). `p53_sequence_comparison_aligned.fasta.gz` contains p53 sequences from
+Plotly's datasets revision `0c447c47b757ad74edecab31f0d72f849d2e67c2`
+(Plotly Technologies Inc., MIT), aligned with MAFFT v7.526 using L-INS-i. The
+corresponding gallery pages describe processing. Copyright notices and terms
+are included in `LICENSES/GALLERY-DATA-MIT.txt`.
 
 ## Code adapted from Vega-Altair
 

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/docs/datasets.md

@@ -1,10 +1,10 @@
 # Example datasets
 
 The combined LAML oncoplot uses `load_dataset("tcga_laml_combined_oncoplot")`;
-the p53 sequence comparison uses `load_dataset("p53_sequence_comparison")`.
-Both return mappings of prepared chart tables, display domains, and source
-provenance. Their MIT-licensed sources, processing, and interpretation limits
-are described in the [combined oncoplot](gallery/combined_laml_oncoplot.md) and
+the p53 sequence comparison loads aligned FASTA text with
+`load_dataset("p53_sequence_comparison", as_format="text")`. Their
+MIT-licensed sources and processing are described in the
+[combined oncoplot](gallery/combined_laml_oncoplot.md) and
 [p53 comparison](gallery/p53_sequence_comparison.md) gallery pages.
 
 The package ships the tables that the [gallery](gallery/index.md) examples use,
@@ -30,7 +30,7 @@ for JSON files. Pass `as_format="text"` to get the raw file contents instead.
 | `tcga_laml_maf` | Somatic mutation calls for TCGA acute myeloid leukemia |
 | `tcga_laml_annotations` | Clinical annotations for those leukemia samples |
 | `tcga_laml_combined_oncoplot` | Prepared mutation, copy-number, clinical, pathway, VAF, and MutSig tables |
-| `p53_sequence_comparison` | 34 unaligned p53 sequences, padded residue tiles, consensus, identity, and coverage |
+| `p53_sequence_comparison` | 34 p53 protein sequences aligned with MAFFT L-INS-i, compressed FASTA |
 | `pyoncoprint_tcga` | Alteration matrix for TCGA lung adenocarcinoma samples |
 | `tcga_ov_gistic_scores` | GISTIC2 copy-number scores for TCGA ovarian tumors |
 | `tcga_ov_gistic_lesions` | GISTIC2 peak regions for the same cohort |

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/docs/examples/brush_linked_genome_tracks.py

@@ -86,7 +86,7 @@ association_track = (
 )
 
 # Show effect sizes for the same range.
-effect_track = (
+effect_points = (
     gs.Chart()
     .mark_point(filled=True, size=24, opacity=0.78, color="#f58518")
     .encode(
@@ -96,10 +96,16 @@ effect_track = (
         y=gs.Y("EFFECTSIZE:Q").scale(domain=[-3, 3]).title("Effect size"),
         tooltip=["SNP:N", "GENE:N", "EFFECTSIZE:Q"],
     )
-    .properties(
-        name="effect-size",
-        height=95,
-    )
+)
+
+# Put a zero line behind the points to separate positive and negative effects.
+effect_baseline = (
+    gs.Chart([{"EFFECTSIZE": 0}])
+    .mark_rule(color="#888888", size=1, tooltip=None)
+    .encode(y=gs.Y("EFFECTSIZE:Q").scale(domain=[-3, 3]).title("Effect size"))
+)
+effect_track = (effect_baseline + effect_points).properties(
+    name="effect-size", height=95
 )
 
 # Add Z-scores as the third view of the selected range.

genome_spy_python-0.3.0/docs/examples/p53_sequence_comparison.md

@@ -0,0 +1,41 @@
+## What to notice
+
+Drag the overview at the bottom to choose the positions shown above. The
+summary tracks, sequence logo, and residue matrix stay aligned as the view
+moves. Move the pointer across the detail tracks to follow one position with
+the vertical ruler. Hover a tile for its accession and position. Zoom in to
+read letters.
+
+**Conservation** shows the fraction of non-gap sequences that share the most
+common amino acid at each alignment column. **Gap-free** shows
+the fraction of sequences containing a residue there. Keeping the two measures
+separate makes it clear whether a low score reflects disagreement or missing
+aligned residues. The sequence logo shows the full non-gap residue mixture,
+with larger letters for larger shares. The x-axis reports one-based alignment
+columns, not residue numbers in any individual protein.
+
+This adapts [Dash Bio AlignmentChart](https://dash.plotly.com/dash-bio/alignmentchart)
+with GenomeSpy rectangles, text, bars, a sequence logo, and a shared brush.
+
+:::{admonition} Data use and provenance
+:class: note
+
+The 34 UniProt-labelled p53 protein sequences come from the
+[Plotly FASTA](https://github.com/plotly/datasets/blob/0c447c47b757ad74edecab31f0d72f849d2e67c2/Dash_Bio/Genetic/alignment_viewer_p53.fasta)
+in Plotly's MIT-licensed datasets repository. They were aligned with MAFFT
+v7.526 using the L-INS-i strategy:
+`mafft-linsi p53.unaligned.fasta > p53.aligned.fasta`. The resulting alignment
+is packaged as `p53_sequence_comparison_aligned.fasta.gz`.
+:::
+
+## Python and GenomeSpy processing
+
+Python reads the packaged compressed FASTA, splits its 34 records, preserves
+the UniProt identifiers and headers, and verifies that every aligned sequence
+has the same length. GenomeSpy then flattens each sequence into residues in the
+browser and declaratively calculates gap-free fractions, non-gap conservation,
+and logo stacks. The Python API authors and serializes
+those transforms; GenomeSpy executes them while rendering and interacting with
+the visualization. For comparison, the
+[multiple sequence alignment example](multiple_sequence_alignment.md) sends
+FASTA directly to GenomeSpy and parses it in the browser-side dataflow.

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/docs/examples/p53_sequence_comparison.py

@@ -1,23 +1,52 @@
-"""P53 sequence comparison with an overview brush.
+"""P53 multiple-sequence alignment with an overview brush.
 
-Explore the p53 FASTA used by Dash Bio, with residue tiles, a consensus logo,
-position agreement, sequence coverage, and a linked overview.
+Explore a MAFFT alignment of the p53 proteins used by Dash Bio, with residue
+tiles, a sequence logo, position agreement, gap prevalence, and a linked
+overview.
 """
 
 import genome_spy as gs
-from genome_spy.datasets import _load_table_bundle as load_data
+from genome_spy.datasets import load_dataset
 
 META = {
     "category": "Reference annotation tracks",
     "order": 29,
-    "height": 870,
+    "height": 850,
     "max_width": 1000,
 }
 
-# Load prepared sequence rows and per-position summaries.
-data = load_data("p53_sequence_comparison", ("cells", "columns"))
-# DataFrames let the gallery store shared tables in separate Arrow files.
-# Use soft amino-acid colors; grey fills the ends of shorter sequences.
+
+def _parse_fasta(text: str) -> list[dict[str, str]]:
+    records = []
+    for block in text.strip().split(">")[1:]:
+        header, *lines = block.splitlines()
+        source_id = header.split(maxsplit=1)[0]
+        parts = source_id.split("|")
+        records.append(
+            {
+                "identifier": parts[-1],
+                "accession": parts[1] if len(parts) >= 3 else source_id,
+                "header": header,
+                "sequence": "".join("".join(lines).split()).upper(),
+            }
+        )
+    if not records:
+        raise ValueError("The FASTA alignment contains no sequences.")
+    lengths = {len(record["sequence"]) for record in records}
+    if len(lengths) != 1:
+        raise ValueError(f"The FASTA sequences are not aligned: lengths={lengths}.")
+    return records
+
+
+# Python handles packaged-file access and the small amount of header parsing.
+alignment_records = _parse_fasta(
+    load_dataset("p53_sequence_comparison", as_format="text")
+)
+alignment_length = len(alignment_records[0]["sequence"])
+sequence_order = [record["identifier"] for record in alignment_records]
+
+# GenomeSpy flattens the sequences and calculates all column-level summaries.
+# Use soft amino-acid colors; alignment gaps are pale grey.
 residue_colors = gs.Scale(
     domain=list("ACDEFGHIKLMNPQRSTVWY-"),
     range=[
@@ -79,17 +108,21 @@ detail_ruler = gs.ruler(
 
 # Keep all positions visible here; drag to choose the range shown below.
 overview = (
-    gs.Chart(data["cells"])
+    gs.Chart()
     .mark_rect()
     .encode(
         x=gs.X("position:I")
-        .scale(domain=[1, data["length"] + 1], zoom=False)
+        .scale(domain=[1, alignment_length + 1], zoom=False)
         .title(None),
-        y=gs.Y("identifier:N")
-        .scale(domain=data["sequence_order"], reverse=True)
-        .axis(None),
+        y=gs.Y("identifier:N").scale(domain=sequence_order, reverse=True).axis(None),
         color=color,
-        tooltip=["identifier:N", "accession:N", "position:Q", "residue:N"],
+        tooltip=[
+            "identifier:N",
+            "accession:N",
+            "position:Q",
+            "residue:N",
+            "header:N",
+        ],
     )
     .properties(height=100)
     .add_params(selection)
@@ -101,28 +134,60 @@ overview_group = (
     .properties(padding=gs.Paddings(top=6))
 )
 
-# Show the fraction matching the most common amino acid at each position.
+# Calculate the most common non-gap residue and its share at each alignment column.
+column_consensus = (
+    gs.Chart()
+    .transform_filter(gs.datum.residue != "-")
+    .transform_aggregate(groupby=["position", "residue"])
+    .transform_window(
+        ops=["sum", "row_number"],
+        fields=["count", None],
+        as_=["nonGapCount", "rank"],
+        frame=[None, None],
+        groupby=["position"],
+        sort=gs.compare(
+            field=["count", "residue"],
+            order=["descending", "ascending"],
+        ),
+    )
+    .transform_filter(gs.datum.rank == 1)
+    .transform_formula(
+        expr=gs.datum.count / gs.datum.nonGapCount,
+        as_="conservation",
+    )
+)
+
+# Show agreement among the non-gap amino acids at each position.
 conservation = (
-    gs.Chart(data["columns"])
-    .mark_rect()
+    column_consensus.mark_rect()
     .encode(
         x=gs.X("position:I").title(None),
-        y=gs.Y("identity:Q").scale(domain=[0, 1]).axis(tickCount=3, title=None),
-        color=gs.Color("identity:Q")
+        y=gs.Y("conservation:Q").scale(domain=[0, 1]).axis(tickCount=3, title=None),
+        color=gs.Color("conservation:Q")
         .scale(domain=[0, 1], scheme="viridis")
         .legend(title="Conservation", gradientLength=140, tickCount=3),
-        tooltip=["position:Q", "identity:Q", "residue:N"],
+        tooltip=["position:Q", "conservation:Q", "residue:N", "nonGapCount:Q"],
     )
     .properties(height=60, title=gs.title("Conservation", style="track-title"))
 )
-# Show the fraction of sequences without a gap at each position.
+# Show the fraction of sequences without a gap at each alignment column.
 gap_free = (
-    gs.Chart(data["columns"])
+    gs.Chart()
+    .transform_formula(
+        expr=gs.expr.if_(gs.datum.residue == "-", 0, 1),
+        as_="hasResidue",
+    )
+    .transform_aggregate(
+        groupby=["position"],
+        fields=["hasResidue"],
+        ops=["mean"],
+        as_=["gapFree"],
+    )
     .mark_rect(color="#b4bbc2")
     .encode(
         x=gs.X("position:I").title(None),
-        y=gs.Y("coverage:Q").scale(domain=[0, 1]).axis(tickCount=3, title=None),
-        tooltip=["position:Q", "coverage:Q"],
+        y=gs.Y("gapFree:Q").scale(domain=[0, 1]).axis(tickCount=3, title=None),
+        tooltip=["position:Q", "gapFree:Q"],
     )
     .properties(
         height=30,
@@ -131,25 +196,9 @@ gap_free = (
     )
 )
 
-# Show the most common amino acid as a compact consensus row.
-consensus_tiles = (
-    gs.Chart(data["columns"])
-    .mark_rect()
-    .encode(
-        x=gs.X("position:I").title(None),
-        y=gs.Y("identifier:N").title(None),
-        color=color,
-        tooltip=["position:Q", "residue:N", "identity:Q"],
-    )
-)
-consensus_letters = consensus_tiles.mark_text(size=11, fitToBand=True).encode(
-    text="residue:N", color=gs.value("#202020")
-)
-consensus = (consensus_tiles + consensus_letters).properties(height=15)
-
 # Summarize the residue mixture at each position as a sequence logo.
-consensus_logo = (
-    gs.Chart(data["cells"])
+sequence_logo = (
+    gs.Chart()
     .transform_filter(gs.datum.residue != "-")
     .transform_aggregate(groupby=["position", "residue"])
     .transform_stack(
@@ -182,15 +231,19 @@ consensus_logo = (
 
 # Draw one colored tile per amino acid, with sequence details on hover.
 tiles = (
-    gs.Chart(data["cells"])
+    gs.Chart()
     .mark_rect()
     .encode(
         x=gs.X("position:I").title(None),
-        y=gs.Y("identifier:N")
-        .scale(domain=data["sequence_order"], reverse=True)
-        .title(None),
+        y=gs.Y("identifier:N").scale(domain=sequence_order, reverse=True).title(None),
         color=legend_color,
-        tooltip=["identifier:N", "accession:N", "position:Q", "residue:N"],
+        tooltip=[
+            "identifier:N",
+            "accession:N",
+            "position:Q",
+            "residue:N",
+            "header:N",
+        ],
     )
 )
 # Add letters when there is enough room to read them.
@@ -204,8 +257,7 @@ details = (
     gs.vconcat(
         gap_free,
         conservation,
-        consensus,
-        consensus_logo,
+        sequence_logo,
         sequences,
         spacing=6,
     )
@@ -228,10 +280,13 @@ chart = (
     gs.vconcat(details, overview_group, spacing=2)
     .add_params(brush)
     .properties(
+        data=alignment_records,
         width="container",
-        title="P53 sequences: overview and residue detail",
-        description="34 original, ungapped p53 sequences from the Dash Bio example. Drag the overview or zoom the detail tracks to compare positions; grey cells pad shorter sequences.",
+        title="P53 protein alignment: overview and residue detail",
+        description="A 34-sequence p53 protein alignment generated with MAFFT L-INS-i. Drag the overview or zoom the detail tracks to compare alignment columns; grey cells are alignment gaps.",
     )
+    .transform_flatten_sequence(as_=["position", "residue"])
+    .transform_formula(expr=gs.datum.position + 1, as_="position")
     .resolve_scale(x="independent", y="independent")
     .resolve_legend(color="collected")
     .configure_legend(

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/notebooks/brush_linked_genome_tracks.ipynb

@@ -9,7 +9,7 @@
     "\n",
     "This notebook makes an interactive genome visualization with [GenomeSpy for Python](https://genomespy.app/genome-spy-python/).\n",
     "\n",
-    "Think of the top track as a **map of the whole genome**. Drag a box across it to choose a region. The three tracks underneath act like magnifying glasses: they all zoom to the region you selected.\n",
+    "Start with a simple plot of p-values. Then add a draggable overview and two more tracks that follow the same selected region.\n",
     "\n",
     "You do not need to know GenomeSpy yet. Run each cell from top to bottom using the play button on its left."
    ]
@@ -109,12 +109,44 @@
     "variants[[\"SNP\", \"chrom\", \"BP\", \"P\", \"EFFECTSIZE\", \"ZSCORE\"]].head()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "first-chart-explanation",
+   "metadata": {},
+   "source": [
+    "## 4. Draw a first chart\n",
+    "\n",
+    "Each point is a variant. Its position comes from `gs.Locus(\"chrom\", \"BP\")`, which combines chromosome and position into one axis. Taller points have smaller p-values. Hover over a point to see its values."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "first-chart",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "association = (\n",
+    "    gs.Chart()\n",
+    "    .mark_point(filled=True, size=24, opacity=0.78, color=\"#4c78a8\")\n",
+    "    .encode(\n",
+    "        x=gs.Locus(\"chrom\", \"BP\"),\n",
+    "        y=gs.Y(\"neglog:Q\").scale(domain=y_domain).title(\"−log10 p\"),\n",
+    "        tooltip=[\"SNP:N\", \"GENE:N\", \"P:Q\"],\n",
+    "    )\n",
+    "    .properties(height=180)\n",
+    ")\n",
+    "\n",
+    "# Give this first chart its data and genome assembly, then show it.\n",
+    "association.properties(data=variants, assembly=\"hg18\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "brush-explanation",
    "metadata": {},
    "source": [
-    "## 4. Make a shared genomic selection\n",
+    "## 5. Add a brush\n",
     "\n",
     "A **brush** is the blue rectangle you draw with the mouse. Its only job is to remember the genomic interval you selected.\n",
     "\n",
@@ -159,11 +191,9 @@
    "id": "overview-explanation",
    "metadata": {},
    "source": [
-    "## 5. Build the whole-genome overview\n",
+    "## 6. Build the whole-genome overview\n",
     "\n",
-    "The `Locus` encoding combines a chromosome column and a position column into one continuous genome-wide axis. That is why points from chromosome 1 through chromosome X can share one x-axis.\n",
-    "\n",
-    "We turn zooming off only for this overview so it always remains our complete genome map."
+    "This smaller, gray plot will sit above our first chart. It stays zoomed out so you can always choose a different region."
    ]
   },
   {
@@ -206,18 +236,18 @@
   },
   {
    "cell_type": "markdown",
-   "id": "details-explanation",
+   "id": "link-explanation",
    "metadata": {},
    "source": [
-    "## 6. Build three detail tracks\n",
+    "## 7. Try the brush with one detail track\n",
     "\n",
-    "Each detail track draws a different measurement, but all three ask the same brush for their x-axis range. Imagine three magnifying glasses tied to the same handle: moving the handle moves all three together."
+    "Reuse the first chart, but let the brush choose its visible range with `gs.SelectionDomainRef`. Drag across the gray overview: the blue chart below follows your selection."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "build-details",
+   "id": "link-first-track",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -227,18 +257,39 @@
     "    initial=initial_region,\n",
     ")\n",
     "\n",
-    "association_track = (\n",
-    "    gs.Chart()\n",
-    "    .mark_point(filled=True, size=24, opacity=0.78, color=\"#4c78a8\")\n",
-    "    .encode(\n",
-    "        x=gs.Locus(\"chrom\", \"BP\").scale(domain=selected_region).axis(None),\n",
-    "        y=gs.Y(\"neglog:Q\").scale(domain=y_domain).title(\"−log10 p\"),\n",
-    "        tooltip=[\"SNP:N\", \"GENE:N\", \"P:Q\"],\n",
-    "    )\n",
-    "    .properties(height=95)\n",
+    "association_track = association.encode(\n",
+    "    x=gs.Locus(\"chrom\", \"BP\").scale(domain=selected_region)\n",
+    ").properties(height=95)\n",
+    "\n",
+    "linked_chart = (\n",
+    "    (overview & association_track)\n",
+    "    .properties(data=variants, assembly=\"hg18\", spacing=8)\n",
+    "    .add_params(brush)\n",
+    "    .resolve_scale(x=\"independent\", y=\"independent\")\n",
+    "    .resolve_axis(x=\"independent\", y=\"independent\")\n",
     ")\n",
     "\n",
-    "effect_track = (\n",
+    "linked_chart"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "details-explanation",
+   "metadata": {},
+   "source": [
+    "## 8. Add two more measurements\n",
+    "\n",
+    "Effect size and Z-score give two more views of the same variants. Both use `selected_region`, so they follow the same brush."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "build-details",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "effect_points = (\n",
     "    gs.Chart()\n",
     "    .mark_point(filled=True, size=24, opacity=0.78, color=\"#f58518\")\n",
     "    .encode(\n",
@@ -246,9 +297,16 @@
     "        y=gs.Y(\"EFFECTSIZE:Q\").scale(domain=[-3, 3]).title(\"Effect size\"),\n",
     "        tooltip=[\"SNP:N\", \"GENE:N\", \"EFFECTSIZE:Q\"],\n",
     "    )\n",
-    "    .properties(height=95)\n",
     ")\n",
     "\n",
+    "# A zero line separates positive and negative effects.\n",
+    "effect_baseline = (\n",
+    "    gs.Chart([{\"EFFECTSIZE\": 0}])\n",
+    "    .mark_rule(color=\"#888888\", size=1, tooltip=None)\n",
+    "    .encode(y=gs.Y(\"EFFECTSIZE:Q\").scale(domain=[-3, 3]).title(\"Effect size\"))\n",
+    ")\n",
+    "effect_track = (effect_baseline + effect_points).properties(height=95)\n",
+    "\n",
     "zscore_track = (\n",
     "    gs.Chart()\n",
     "    .mark_point(filled=True, size=24, opacity=0.78, color=\"#54a24b\")\n",
@@ -266,7 +324,7 @@
    "id": "display-explanation",
    "metadata": {},
    "source": [
-    "## 7. Stack the tracks and try the chart\n",
+    "## 9. Put it all together\n",
     "\n",
     "`vconcat` stacks charts vertically. The whole composition receives the same data, genome assembly, and brush parameter.\n",
     "\n",
@@ -286,7 +344,15 @@
    "outputs": [],
    "source": [
     "chart = (\n",
-    "    gs.vconcat(overview, association_track, effect_track, zscore_track)\n",
+    "    gs.vconcat(\n",
+    "        overview,\n",
+    "        # Only the bottom detail track needs x-axis labels.\n",
+    "        association_track.encode(\n",
+    "            x=gs.Locus(\"chrom\", \"BP\").scale(domain=selected_region).axis(None)\n",
+    "        ),\n",
+    "        effect_track,\n",
+    "        zscore_track,\n",
+    "    )\n",
     "    .properties(\n",
     "        data=variants,\n",
     "        assembly=\"hg18\",\n",

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "genome-spy-python"
-version = "0.2.0"
+version = "0.3.0"
 description = "genome-spy-python is a declarative genomics visualization library for Python, built on top of the genome-spy JSON specification."
 readme = "README.md"
 requires-python = ">=3.11"

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/src/genome_spy/__init__.py

@@ -196,4 +196,4 @@ __all__ = [
     # END GENERATED INTERACTION EXPORTS
 ]
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/src/genome_spy/datasets/__init__.py

@@ -21,7 +21,7 @@ _DATASETS = {
     "brca_maf": "brca.maf.gz",
     "hapmap_gwas": "hapmap_gwas.csv",
     "mutation_impact_reference": "mutation_impact_reference.json",
-    "p53_sequence_comparison": "p53_sequence_comparison.json.gz",
+    "p53_sequence_comparison": "p53_sequence_comparison_aligned.fasta.gz",
     "pik3ca_mutations": "pik3ca_mutations.json",
     "pik3ca_tcga_brca_lollipop": "pik3ca_tcga_brca_lollipop.json",
     "tal1_alphagenome_reference": "tal1_alphagenome_reference.json.gz",

{genome_spy_python-0.2.0 → genome_spy_python-0.3.0}/tests/test_chart.py

@@ -57,7 +57,7 @@ from genome_spy.schemapi import SchemaBase, SchemaValidationError
 
 
 def test_package_exposes_version() -> None:
-    assert gs.__version__ == "0.2.0"
+    assert gs.__version__ == "0.3.0"
 
 
 def test_public_api_exports_are_unique() -> None: