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Add notebooks to docs (#426)
* Add notebooks to docs * Update nb titles
1 parent 28f0e38 commit 88d6d85

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-225
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‎docs/notebooks/page_mode_example.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Page mode example"
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"# Page mode example"
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]
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},
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{
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"vw = vc.widget(page_esm=PAGE_ESM, page_mode=True, height=1100)\n",
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"vw"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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],
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"metadata": {

‎docs/notebooks/spatial_data.ipynb‎

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"vw = vc.widget()\n",
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"vw"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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"metadata": {

‎docs/notebooks/spatial_data_blobs.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of a SpatialData object"
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"# Visualization of a SpatialData object, blobs example"
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]
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},
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{
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"vw = vc.widget()\n",
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"vw"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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],
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"metadata": {

‎docs/notebooks/spatial_data_mouseliver.ipynb‎

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{
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"cell_type": "markdown",
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"metadata": {
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"nbsphinx": "hidden",
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"nbsphinx": "hidden"
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},
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"source": [
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"# Vitessce Widget Tutorial"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"tags": []
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},
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"source": [
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"# Interactive visualization of spatial single-cell data using Vitessce"
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"# Visualization of a SpatialData object and individual Spatial Elements, local data"
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]
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},
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{
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"tags": []
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},
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"source": [
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"# Visualization of a SpatialData object"
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"## Visualization of a SpatialData object"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of an AnnData object"
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"## Visualization of an AnnData object"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of an image file"
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"## Visualization of an image file"
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]
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},
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{
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"Note that the `_store` options are only available for Zarr-based formats, such as AnnDataWrapper, SpatialDataWrapper, and ImageOmeZarrWrapper.\n",
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"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."
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]
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"metadata": {

‎docs/notebooks/spatial_data_mouseliver_remote.ipynb‎

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"tags": []
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},
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"source": [
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"# Interactive visualization of spatial single-cell data using Vitessce"
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"# Vitessce Widget Tutorial"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"tags": []
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},
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"source": [
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"# Visualization of a SpatialData object and individual Spatial Elements, remote data"
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]
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},
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{
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"tags": []
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},
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"source": [
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"# Visualization of a SpatialData object"
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"## Visualization of a SpatialData object"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of an AnnData object"
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"## Visualization of an AnnData object"
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]
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of an image file"
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"## Visualization of an image file"
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]
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{
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"Note that the `_store` options are only available for Zarr-based formats, such as AnnDataWrapper, SpatialDataWrapper, and ImageOmeZarrWrapper.\n",
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"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."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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],
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"metadata": {

‎docs/notebooks/web_app_brain.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of single-cell RNA seq data"
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"# Visualization of single-cell RNA seq data using vitessce.io"
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]
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},
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{
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"source": [
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"vc.web_app()"
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]
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},
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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"metadata": {},
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"outputs": [],
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"source": []
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"metadata": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.0"
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"version": "3.10.14"
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}
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},
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"nbformat": 4,

‎docs/notebooks/widget_brain_h5ad.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of single-cell RNA seq data"
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"# Visualization of single-cell RNA seq data from H5AD file"
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]
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{
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"vw = vc.widget()\n",
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"vw"
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"metadata": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.0"
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"version": "3.10.14"
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}
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"nbformat": 4,

‎docs/notebooks/widget_brain_with_base_dir.ipynb‎

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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.0"
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"version": "3.10.14"
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}
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"nbformat": 4,

‎docs/notebooks/widget_modify_config.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"cell_type": "markdown",
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"metadata": {
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"colab": {
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"base_uri": "https://localhost:8080/"
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},
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"id": "zLOtLwy1cb39",
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"outputId": "dc04a9c7-6a79-466a-97ac-5f6d68299bcb",
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"tags": []
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"id": "dI4N5oh0cYc1",
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"nbsphinx": "hidden"
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},
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"outputs": [],
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"source": [
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"!pip install \"vitessce[all]\""
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"# Vitessce Widget Tutorial"
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]
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},
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{
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"cell_type": "markdown",
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"id": "dI4N5oh0cYc1",
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"nbsphinx": "hidden"
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"metadata": {},
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"source": [
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"# Vitessce Widget Tutorial"
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"# Programmatic modification of widget configuration"
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" }\n",
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"}"
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"id": "0M7PelaPdyBY"
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"metadata": {

‎docs/notebooks/widget_pbmc_remote.ipynb‎

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"vw = vc.widget()\n",
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"vw"
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.0"
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"version": "3.10.14"
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}
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},
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"nbformat": 4,

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