Skip to content

Commit 88d6d85

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

15 files changed

+98
-225
lines changed

docs/notebooks/page_mode_example.ipynb

Lines changed: 1 addition & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
"cell_type": "markdown",
1414
"metadata": {},
1515
"source": [
16-
"## Page mode example"
16+
"# Page mode example"
1717
]
1818
},
1919
{
@@ -171,27 +171,6 @@
171171
"vw = vc.widget(page_esm=PAGE_ESM, page_mode=True, height=1100)\n",
172172
"vw"
173173
]
174-
},
175-
{
176-
"cell_type": "code",
177-
"execution_count": null,
178-
"metadata": {},
179-
"outputs": [],
180-
"source": []
181-
},
182-
{
183-
"cell_type": "code",
184-
"execution_count": null,
185-
"metadata": {},
186-
"outputs": [],
187-
"source": []
188-
},
189-
{
190-
"cell_type": "code",
191-
"execution_count": null,
192-
"metadata": {},
193-
"outputs": [],
194-
"source": []
195174
}
196175
],
197176
"metadata": {

docs/notebooks/spatial_data.ipynb

Lines changed: 0 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -138,13 +138,6 @@
138138
"vw = vc.widget()\n",
139139
"vw"
140140
]
141-
},
142-
{
143-
"cell_type": "code",
144-
"execution_count": null,
145-
"metadata": {},
146-
"outputs": [],
147-
"source": []
148141
}
149142
],
150143
"metadata": {

docs/notebooks/spatial_data_blobs.ipynb

Lines changed: 1 addition & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
"cell_type": "markdown",
1414
"metadata": {},
1515
"source": [
16-
"# Visualization of a SpatialData object"
16+
"# Visualization of a SpatialData object, blobs example"
1717
]
1818
},
1919
{
@@ -185,20 +185,6 @@
185185
"vw = vc.widget()\n",
186186
"vw"
187187
]
188-
},
189-
{
190-
"cell_type": "code",
191-
"execution_count": null,
192-
"metadata": {},
193-
"outputs": [],
194-
"source": []
195-
},
196-
{
197-
"cell_type": "code",
198-
"execution_count": null,
199-
"metadata": {},
200-
"outputs": [],
201-
"source": []
202188
}
203189
],
204190
"metadata": {

docs/notebooks/spatial_data_mouseliver.ipynb

Lines changed: 13 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -3,11 +3,19 @@
33
{
44
"cell_type": "markdown",
55
"metadata": {
6-
"nbsphinx": "hidden",
6+
"nbsphinx": "hidden"
7+
},
8+
"source": [
9+
"# Vitessce Widget Tutorial"
10+
]
11+
},
12+
{
13+
"cell_type": "markdown",
14+
"metadata": {
715
"tags": []
816
},
917
"source": [
10-
"# Interactive visualization of spatial single-cell data using Vitessce"
18+
"# Visualization of a SpatialData object and individual Spatial Elements, local data"
1119
]
1220
},
1321
{
@@ -206,7 +214,7 @@
206214
"tags": []
207215
},
208216
"source": [
209-
"# Visualization of a SpatialData object"
217+
"## Visualization of a SpatialData object"
210218
]
211219
},
212220
{
@@ -410,7 +418,7 @@
410418
"cell_type": "markdown",
411419
"metadata": {},
412420
"source": [
413-
"# Visualization of an AnnData object"
421+
"## Visualization of an AnnData object"
414422
]
415423
},
416424
{
@@ -589,7 +597,7 @@
589597
"cell_type": "markdown",
590598
"metadata": {},
591599
"source": [
592-
"# Visualization of an image file"
600+
"## Visualization of an image file"
593601
]
594602
},
595603
{
@@ -755,13 +763,6 @@
755763
"Note that the `_store` options are only available for Zarr-based formats, such as AnnDataWrapper, SpatialDataWrapper, and ImageOmeZarrWrapper.\n",
756764
"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."
757765
]
758-
},
759-
{
760-
"cell_type": "code",
761-
"execution_count": null,
762-
"metadata": {},
763-
"outputs": [],
764-
"source": []
765766
}
766767
],
767768
"metadata": {

docs/notebooks/spatial_data_mouseliver_remote.ipynb

Lines changed: 14 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,16 @@
77
"tags": []
88
},
99
"source": [
10-
"# Interactive visualization of spatial single-cell data using Vitessce"
10+
"# Vitessce Widget Tutorial"
11+
]
12+
},
13+
{
14+
"cell_type": "markdown",
15+
"metadata": {
16+
"tags": []
17+
},
18+
"source": [
19+
"# Visualization of a SpatialData object and individual Spatial Elements, remote data"
1120
]
1221
},
1322
{
@@ -50,7 +59,7 @@
5059
},
5160
{
5261
"cell_type": "code",
53-
"execution_count": null,
62+
"execution_count": 1,
5463
"metadata": {},
5564
"outputs": [],
5665
"source": [
@@ -169,7 +178,7 @@
169178
"tags": []
170179
},
171180
"source": [
172-
"# Visualization of a SpatialData object"
181+
"## Visualization of a SpatialData object"
173182
]
174183
},
175184
{
@@ -324,7 +333,7 @@
324333
"cell_type": "markdown",
325334
"metadata": {},
326335
"source": [
327-
"# Visualization of an AnnData object"
336+
"## Visualization of an AnnData object"
328337
]
329338
},
330339
{
@@ -426,7 +435,7 @@
426435
"cell_type": "markdown",
427436
"metadata": {},
428437
"source": [
429-
"# Visualization of an image file"
438+
"## Visualization of an image file"
430439
]
431440
},
432441
{
@@ -592,27 +601,6 @@
592601
"Note that the `_store` options are only available for Zarr-based formats, such as AnnDataWrapper, SpatialDataWrapper, and ImageOmeZarrWrapper.\n",
593602
"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."
594603
]
595-
},
596-
{
597-
"cell_type": "code",
598-
"execution_count": null,
599-
"metadata": {},
600-
"outputs": [],
601-
"source": []
602-
},
603-
{
604-
"cell_type": "code",
605-
"execution_count": null,
606-
"metadata": {},
607-
"outputs": [],
608-
"source": []
609-
},
610-
{
611-
"cell_type": "code",
612-
"execution_count": null,
613-
"metadata": {},
614-
"outputs": [],
615-
"source": []
616604
}
617605
],
618606
"metadata": {

docs/notebooks/web_app_brain.ipynb

Lines changed: 2 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
"cell_type": "markdown",
1414
"metadata": {},
1515
"source": [
16-
"# Visualization of single-cell RNA seq data"
16+
"# Visualization of single-cell RNA seq data using vitessce.io"
1717
]
1818
},
1919
{
@@ -227,20 +227,6 @@
227227
"source": [
228228
"vc.web_app()"
229229
]
230-
},
231-
{
232-
"cell_type": "code",
233-
"execution_count": null,
234-
"metadata": {},
235-
"outputs": [],
236-
"source": []
237-
},
238-
{
239-
"cell_type": "code",
240-
"execution_count": null,
241-
"metadata": {},
242-
"outputs": [],
243-
"source": []
244230
}
245231
],
246232
"metadata": {
@@ -259,7 +245,7 @@
259245
"name": "python",
260246
"nbconvert_exporter": "python",
261247
"pygments_lexer": "ipython3",
262-
"version": "3.8.0"
248+
"version": "3.10.14"
263249
}
264250
},
265251
"nbformat": 4,

docs/notebooks/widget_brain_h5ad.ipynb

Lines changed: 2 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
"cell_type": "markdown",
1414
"metadata": {},
1515
"source": [
16-
"# Visualization of single-cell RNA seq data"
16+
"# Visualization of single-cell RNA seq data from H5AD file"
1717
]
1818
},
1919
{
@@ -144,13 +144,6 @@
144144
"vw = vc.widget()\n",
145145
"vw"
146146
]
147-
},
148-
{
149-
"cell_type": "code",
150-
"execution_count": null,
151-
"metadata": {},
152-
"outputs": [],
153-
"source": []
154147
}
155148
],
156149
"metadata": {
@@ -169,7 +162,7 @@
169162
"name": "python",
170163
"nbconvert_exporter": "python",
171164
"pygments_lexer": "ipython3",
172-
"version": "3.9.0"
165+
"version": "3.10.14"
173166
}
174167
},
175168
"nbformat": 4,

docs/notebooks/widget_brain_with_base_dir.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -321,7 +321,7 @@
321321
"name": "python",
322322
"nbconvert_exporter": "python",
323323
"pygments_lexer": "ipython3",
324-
"version": "3.9.0"
324+
"version": "3.10.14"
325325
}
326326
},
327327
"nbformat": 4,

docs/notebooks/widget_modify_config.ipynb

Lines changed: 6 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -1,29 +1,20 @@
11
{
22
"cells": [
33
{
4-
"cell_type": "code",
5-
"execution_count": null,
4+
"cell_type": "markdown",
65
"metadata": {
7-
"colab": {
8-
"base_uri": "https://localhost:8080/"
9-
},
10-
"id": "zLOtLwy1cb39",
11-
"outputId": "dc04a9c7-6a79-466a-97ac-5f6d68299bcb",
12-
"tags": []
6+
"id": "dI4N5oh0cYc1",
7+
"nbsphinx": "hidden"
138
},
14-
"outputs": [],
159
"source": [
16-
"!pip install \"vitessce[all]\""
10+
"# Vitessce Widget Tutorial"
1711
]
1812
},
1913
{
2014
"cell_type": "markdown",
21-
"metadata": {
22-
"id": "dI4N5oh0cYc1",
23-
"nbsphinx": "hidden"
24-
},
15+
"metadata": {},
2516
"source": [
26-
"# Vitessce Widget Tutorial"
17+
"# Programmatic modification of widget configuration"
2718
]
2819
},
2920
{
@@ -157,15 +148,6 @@
157148
" }\n",
158149
"}"
159150
]
160-
},
161-
{
162-
"cell_type": "code",
163-
"execution_count": null,
164-
"metadata": {
165-
"id": "0M7PelaPdyBY"
166-
},
167-
"outputs": [],
168-
"source": []
169151
}
170152
],
171153
"metadata": {

docs/notebooks/widget_pbmc_remote.ipynb

Lines changed: 1 addition & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -113,20 +113,6 @@
113113
"vw = vc.widget()\n",
114114
"vw"
115115
]
116-
},
117-
{
118-
"cell_type": "code",
119-
"execution_count": null,
120-
"metadata": {},
121-
"outputs": [],
122-
"source": []
123-
},
124-
{
125-
"cell_type": "code",
126-
"execution_count": null,
127-
"metadata": {},
128-
"outputs": [],
129-
"source": []
130116
}
131117
],
132118
"metadata": {
@@ -145,7 +131,7 @@
145131
"name": "python",
146132
"nbconvert_exporter": "python",
147133
"pygments_lexer": "ipython3",
148-
"version": "3.8.0"
134+
"version": "3.10.14"
149135
}
150136
},
151137
"nbformat": 4,

0 commit comments

Comments
 (0)