diff --git a/docs/notebooks/page_mode_example.ipynb b/docs/notebooks/page_mode_example.ipynb index 7b0fa2ec..031111c8 100644 --- a/docs/notebooks/page_mode_example.ipynb +++ b/docs/notebooks/page_mode_example.ipynb @@ -13,7 +13,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Page mode example" + "# Page mode example" ] }, { @@ -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": { diff --git a/docs/notebooks/spatial_data.ipynb b/docs/notebooks/spatial_data.ipynb index d516f96a..0da858d7 100644 --- a/docs/notebooks/spatial_data.ipynb +++ b/docs/notebooks/spatial_data.ipynb @@ -138,13 +138,6 @@ "vw = vc.widget()\n", "vw" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/docs/notebooks/spatial_data_blobs.ipynb b/docs/notebooks/spatial_data_blobs.ipynb index 98d4650b..d2ce9e7b 100644 --- a/docs/notebooks/spatial_data_blobs.ipynb +++ b/docs/notebooks/spatial_data_blobs.ipynb @@ -13,7 +13,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualization of a SpatialData object" + "# Visualization of a SpatialData object, blobs example" ] }, { @@ -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": { diff --git a/docs/notebooks/spatial_data_mouseliver.ipynb b/docs/notebooks/spatial_data_mouseliver.ipynb index a4603ef9..a7b90169 100644 --- a/docs/notebooks/spatial_data_mouseliver.ipynb +++ b/docs/notebooks/spatial_data_mouseliver.ipynb @@ -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" ] }, { @@ -206,7 +214,7 @@ "tags": [] }, "source": [ - "# Visualization of a SpatialData object" + "## Visualization of a SpatialData object" ] }, { @@ -410,7 +418,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualization of an AnnData object" + "## Visualization of an AnnData object" ] }, { @@ -589,7 +597,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualization of an image file" + "## Visualization of an image file" ] }, { @@ -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": { diff --git a/docs/notebooks/spatial_data_mouseliver_remote.ipynb b/docs/notebooks/spatial_data_mouseliver_remote.ipynb index 5f81a953..ba35eb99 100644 --- a/docs/notebooks/spatial_data_mouseliver_remote.ipynb +++ b/docs/notebooks/spatial_data_mouseliver_remote.ipynb @@ -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" ] }, { @@ -50,7 +59,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -169,7 +178,7 @@ "tags": [] }, "source": [ - "# Visualization of a SpatialData object" + "## Visualization of a SpatialData object" ] }, { @@ -324,7 +333,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualization of an AnnData object" + "## Visualization of an AnnData object" ] }, { @@ -426,7 +435,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualization of an image file" + "## Visualization of an image file" ] }, { @@ -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": { diff --git a/docs/notebooks/web_app_brain.ipynb b/docs/notebooks/web_app_brain.ipynb index 85d7905e..bd3d6eb0 100644 --- a/docs/notebooks/web_app_brain.ipynb +++ b/docs/notebooks/web_app_brain.ipynb @@ -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" ] }, { @@ -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": { @@ -259,7 +245,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.0" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/notebooks/widget_brain_h5ad.ipynb b/docs/notebooks/widget_brain_h5ad.ipynb index d3a37359..66183ceb 100644 --- a/docs/notebooks/widget_brain_h5ad.ipynb +++ b/docs/notebooks/widget_brain_h5ad.ipynb @@ -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" ] }, { @@ -144,13 +144,6 @@ "vw = vc.widget()\n", "vw" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -169,7 +162,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/notebooks/widget_brain_with_base_dir.ipynb b/docs/notebooks/widget_brain_with_base_dir.ipynb index 015a3e67..41da8211 100644 --- a/docs/notebooks/widget_brain_with_base_dir.ipynb +++ b/docs/notebooks/widget_brain_with_base_dir.ipynb @@ -321,7 +321,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/notebooks/widget_modify_config.ipynb b/docs/notebooks/widget_modify_config.ipynb index be288022..97355f6d 100644 --- a/docs/notebooks/widget_modify_config.ipynb +++ b/docs/notebooks/widget_modify_config.ipynb @@ -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" ] }, { @@ -157,15 +148,6 @@ " }\n", "}" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "id": "0M7PelaPdyBY" - }, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/docs/notebooks/widget_pbmc_remote.ipynb b/docs/notebooks/widget_pbmc_remote.ipynb index d238dca7..5b9101c8 100644 --- a/docs/notebooks/widget_pbmc_remote.ipynb +++ b/docs/notebooks/widget_pbmc_remote.ipynb @@ -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": { @@ -145,7 +131,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.0" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/notebooks/widget_plugin_custom.ipynb b/docs/notebooks/widget_plugin_custom.ipynb index c8c44e14..c8b19f85 100644 --- a/docs/notebooks/widget_plugin_custom.ipynb +++ b/docs/notebooks/widget_plugin_custom.ipynb @@ -9,6 +9,13 @@ "# Vitessce Widget Tutorial" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Vitessce custom plugin definition" + ] + }, { "cell_type": "code", "execution_count": null, @@ -151,13 +158,6 @@ "vw = vc.widget(plugins=[ChatPlugin()])\n", "vw" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/docs/notebooks/widget_plugin_demo.ipynb b/docs/notebooks/widget_plugin_demo.ipynb index 9fd0a419..ca25fe1c 100644 --- a/docs/notebooks/widget_plugin_demo.ipynb +++ b/docs/notebooks/widget_plugin_demo.ipynb @@ -13,7 +13,13 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualization of Multi-Modal Imaging Data\n", + "# Vitessce plugin usage demo" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ "We visualize IMS, PAS, and AF imaging data overlaid from the Spraggins Lab of the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University, uploaded to the HuBMAP data portal." ] }, @@ -85,34 +91,11 @@ "cell_type": "code", "execution_count": 4, "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "837fec6d047c4f83be8530996e324fb9", - "version_major": 2, - "version_minor": 1 - }, - "text/plain": [ - "VitessceWidget(config={'version': '1.0.15', 'name': 'Spraggins Multi-Modal', 'description': 'PAS + IMS + AF Fr…" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "vw = vc.widget(plugins=[DemoPlugin()])\n", "vw" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -131,7 +114,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/notebooks/widget_plugin_spatial-query.ipynb b/docs/notebooks/widget_plugin_spatial-query.ipynb index 88d28bf0..c204f834 100644 --- a/docs/notebooks/widget_plugin_spatial-query.ipynb +++ b/docs/notebooks/widget_plugin_spatial-query.ipynb @@ -1,5 +1,21 @@ { "cells": [ + { + "cell_type": "markdown", + "metadata": { + "nbsphinx": "hidden" + }, + "source": [ + "# Vitessce Widget Tutorial" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Vitessce SpatialQuery plugin usage demo" + ] + }, { "cell_type": "code", "execution_count": null, @@ -105,44 +121,11 @@ "cell_type": "code", "execution_count": 13, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/mkeller/software/miniconda3/envs/vitessce-python-notebooks/lib/python3.9/site-packages/traitlets/traitlets.py:869: DeprecationWarning: Deprecated in traitlets 4.1, use the instance .metadata dictionary directly, like x.metadata[key] or x.metadata.get(key, default)\n", - " warn(\"Deprecated in traitlets 4.1, \" + msg, DeprecationWarning, stacklevel=2)\n", - "/Users/mkeller/software/miniconda3/envs/vitessce-python-notebooks/lib/python3.9/site-packages/traitlets/traitlets.py:869: DeprecationWarning: Deprecated in traitlets 4.1, use the instance .metadata dictionary directly, like x.metadata[key] or x.metadata.get(key, default)\n", - " warn(\"Deprecated in traitlets 4.1, \" + msg, DeprecationWarning, stacklevel=2)\n" - ] - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "6f30fb3eac1644478df256bf79a986e9", - "version_major": 2, - "version_minor": 1 - }, - "text/plain": [ - "VitessceWidget(config={'version': '1.0.16', 'name': 'Spatial-Query', 'description': '', 'datasets': [{'uid': '…" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "vw = vc.widget(height=900, plugins=[plugin], remount_on_uid_change=False)\n", "vw" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -161,7 +144,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/notebooks/widget_segmentations_beta.ipynb b/docs/notebooks/widget_segmentations_beta.ipynb index 6c82c420..d398414f 100644 --- a/docs/notebooks/widget_segmentations_beta.ipynb +++ b/docs/notebooks/widget_segmentations_beta.ipynb @@ -9,6 +9,13 @@ "# Vitessce Widget Tutorial" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Visualization of OME-TIFF images and segmentation masks" + ] + }, { "cell_type": "code", "execution_count": null, @@ -71,13 +78,6 @@ "vw = vc.widget()\n", "vw" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -96,7 +96,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/widget_examples.rst b/docs/widget_examples.rst index 173af5a4..4e81237c 100644 --- a/docs/widget_examples.rst +++ b/docs/widget_examples.rst @@ -2,12 +2,25 @@ Widget examples ############### .. toctree:: - :maxdepth: 2 + :maxdepth: 1 notebooks/widget_brain + notebooks/widget_brain_h5ad + notebooks/widget_brain_with_base_dir + notebooks/web_app_brain notebooks/widget_genomic_profiles notebooks/widget_imaging + notebooks/widget_segmentations_beta notebooks/widget_pbmc + notebooks/widget_pbmc_remote + notebooks/spatial_data + notebooks/spatial_data_blobs + notebooks/spatial_data_mouseliver + notebooks/spatial_data_mouseliver_remote notebooks/widget_loom notebooks/widget_from_dict - notebooks/widget_pbmc_remote.ipynb \ No newline at end of file + notebooks/widget_modify_config + notebooks/widget_plugin_demo + notebooks/widget_plugin_custom + notebooks/widget_plugin_spatial-query + notebooks/page_mode_example