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May 15, 2025
Merged

Add notebooks to docs #426

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3173532
Add notebooks to docs
keller-mark May 15, 2025
75d43ca
Update nb titles
keller-mark May 15, 2025
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23 changes: 1 addition & 22 deletions docs/notebooks/page_mode_example.ipynb
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Expand Up @@ -13,7 +13,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Page mode example"
"# Page mode example"
]
},
{
Expand Down Expand Up @@ -171,27 +171,6 @@
"vw = vc.widget(page_esm=PAGE_ESM, page_mode=True, height=1100)\n",
"vw"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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7 changes: 0 additions & 7 deletions docs/notebooks/spatial_data.ipynb
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Expand Up @@ -138,13 +138,6 @@
"vw = vc.widget()\n",
"vw"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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16 changes: 1 addition & 15 deletions docs/notebooks/spatial_data_blobs.ipynb
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Expand Up @@ -13,7 +13,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Visualization of a SpatialData object"
"# Visualization of a SpatialData object, blobs example"
]
},
{
Expand Down Expand Up @@ -185,20 +185,6 @@
"vw = vc.widget()\n",
"vw"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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25 changes: 13 additions & 12 deletions docs/notebooks/spatial_data_mouseliver.ipynb
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Expand Up @@ -3,11 +3,19 @@
{
"cell_type": "markdown",
"metadata": {
"nbsphinx": "hidden",
"nbsphinx": "hidden"
},
"source": [
"# Vitessce Widget Tutorial"
]
},
{
"cell_type": "markdown",
"metadata": {
"tags": []
},
"source": [
"# Interactive visualization of spatial single-cell data using Vitessce"
"# Visualization of a SpatialData object and individual Spatial Elements, local data"
]
},
{
Expand Down Expand Up @@ -206,7 +214,7 @@
"tags": []
},
"source": [
"# Visualization of a SpatialData object"
"## Visualization of a SpatialData object"
]
},
{
Expand Down Expand Up @@ -410,7 +418,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Visualization of an AnnData object"
"## Visualization of an AnnData object"
]
},
{
Expand Down Expand Up @@ -589,7 +597,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Visualization of an image file"
"## Visualization of an image file"
]
},
{
Expand Down Expand Up @@ -755,13 +763,6 @@
"Note that the `_store` options are only available for Zarr-based formats, such as AnnDataWrapper, SpatialDataWrapper, and ImageOmeZarrWrapper.\n",
"Further, when multiple files are required, such as both `adata_path` and `ref_path` (for the JSON reference specification file accompanying an H5AD file) or `img_path` and `offsets_path`, multiple parameter suffices may need to be changed."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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40 changes: 14 additions & 26 deletions docs/notebooks/spatial_data_mouseliver_remote.ipynb
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Expand Up @@ -7,7 +7,16 @@
"tags": []
},
"source": [
"# Interactive visualization of spatial single-cell data using Vitessce"
"# Vitessce Widget Tutorial"
]
},
{
"cell_type": "markdown",
"metadata": {
"tags": []
},
"source": [
"# Visualization of a SpatialData object and individual Spatial Elements, remote data"
]
},
{
Expand Down Expand Up @@ -50,7 +59,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -169,7 +178,7 @@
"tags": []
},
"source": [
"# Visualization of a SpatialData object"
"## Visualization of a SpatialData object"
]
},
{
Expand Down Expand Up @@ -324,7 +333,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Visualization of an AnnData object"
"## Visualization of an AnnData object"
]
},
{
Expand Down Expand Up @@ -426,7 +435,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Visualization of an image file"
"## Visualization of an image file"
]
},
{
Expand Down Expand Up @@ -592,27 +601,6 @@
"Note that the `_store` options are only available for Zarr-based formats, such as AnnDataWrapper, SpatialDataWrapper, and ImageOmeZarrWrapper.\n",
"Further, when multiple files are required, such as both `adata_path` and `ref_path` (for the JSON reference specification file accompanying an H5AD file) or `img_path` and `offsets_path`, multiple parameter suffices may need to be changed."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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18 changes: 2 additions & 16 deletions docs/notebooks/web_app_brain.ipynb
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Expand Up @@ -13,7 +13,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Visualization of single-cell RNA seq data"
"# Visualization of single-cell RNA seq data using vitessce.io"
]
},
{
Expand Down Expand Up @@ -227,20 +227,6 @@
"source": [
"vc.web_app()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -259,7 +245,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.0"
"version": "3.10.14"
}
},
"nbformat": 4,
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11 changes: 2 additions & 9 deletions docs/notebooks/widget_brain_h5ad.ipynb
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Expand Up @@ -13,7 +13,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Visualization of single-cell RNA seq data"
"# Visualization of single-cell RNA seq data from H5AD file"
]
},
{
Expand Down Expand Up @@ -144,13 +144,6 @@
"vw = vc.widget()\n",
"vw"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -169,7 +162,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.0"
"version": "3.10.14"
}
},
"nbformat": 4,
Expand Down
2 changes: 1 addition & 1 deletion docs/notebooks/widget_brain_with_base_dir.ipynb
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Expand Up @@ -321,7 +321,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.0"
"version": "3.10.14"
}
},
"nbformat": 4,
Expand Down
30 changes: 6 additions & 24 deletions docs/notebooks/widget_modify_config.ipynb
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@@ -1,29 +1,20 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"cell_type": "markdown",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "zLOtLwy1cb39",
"outputId": "dc04a9c7-6a79-466a-97ac-5f6d68299bcb",
"tags": []
"id": "dI4N5oh0cYc1",
"nbsphinx": "hidden"
},
"outputs": [],
"source": [
"!pip install \"vitessce[all]\""
"# Vitessce Widget Tutorial"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "dI4N5oh0cYc1",
"nbsphinx": "hidden"
},
"metadata": {},
"source": [
"# Vitessce Widget Tutorial"
"# Programmatic modification of widget configuration"
]
},
{
Expand Down Expand Up @@ -157,15 +148,6 @@
" }\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "0M7PelaPdyBY"
},
"outputs": [],
"source": []
}
],
"metadata": {
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16 changes: 1 addition & 15 deletions docs/notebooks/widget_pbmc_remote.ipynb
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Expand Up @@ -113,20 +113,6 @@
"vw = vc.widget()\n",
"vw"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -145,7 +131,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.0"
"version": "3.10.14"
}
},
"nbformat": 4,
Expand Down
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