Skip to content

Commit 671b81b

Browse files
lambdamoseslambdamoses
committed
Annoying jupyter stuff
Merge branch 'documentation' of https://github.com/pachterlab/voyager into documentation # Conflicts: # vignettes/bivariate.ipynb # vignettes/create_sfe.ipynb # vignettes/create_sfe_v2.ipynb # vignettes/localc.ipynb # vignettes/multispati.ipynb # vignettes/nonspatial.ipynb # vignettes/preprocess_10xv3.ipynb # vignettes/preprocess_atac.ipynb # vignettes/preprocess_clicktag.ipynb # vignettes/preprocess_crispr.ipynb # vignettes/preprocess_multiome.ipynb # vignettes/preprocess_nuclei.ipynb # vignettes/preprocess_splitseq.ipynb # vignettes/preprocess_visium.ipynb # vignettes/sfemethod.ipynb # vignettes/variogram.ipynb # vignettes/vig10_10x_nuclei.ipynb # vignettes/vig11_clicktags.ipynb # vignettes/vig12_crispr.ipynb # vignettes/vig13_10xatac.ipynb # vignettes/vig14_10xmultiome.ipynb # vignettes/vig1_visium_basic.ipynb # vignettes/vig2_visium.ipynb # vignettes/vig3_slideseq_v2.ipynb # vignettes/vig4_cosmx.ipynb # vignettes/vig5_xenium.ipynb # vignettes/vig6_merfish.ipynb # vignettes/vig7_seqfish.ipynb # vignettes/vig8_codex.ipynb # vignettes/vig9_splitseq.ipynb # vignettes/visium_10x.ipynb # vignettes/visium_10x_spatial.ipynb
2 parents 42792c9 + c9ed93f commit 671b81b

32 files changed

+6657
-333
lines changed

‎vignettes/bivariate.ipynb

+196
Large diffs are not rendered by default.

‎vignettes/create_sfe.ipynb

+180
Large diffs are not rendered by default.

‎vignettes/create_sfe_v2.ipynb

+72
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
33
{
44
"cell_type": "raw",
55
<<<<<<< HEAD
6+
<<<<<<< HEAD
67
<<<<<<< HEAD
78
"id": "f7bed1d2",
89
=======
@@ -11,6 +12,9 @@
1112
=======
1213
"id": "22aa3a6b",
1314
>>>>>>> documentation-devel
15+
=======
16+
"id": "121642d2",
17+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
1418
"metadata": {},
1519
"source": [
1620
"---\n",
@@ -35,6 +39,7 @@
3539
"cell_type": "code",
3640
"execution_count": null,
3741
<<<<<<< HEAD
42+
<<<<<<< HEAD
3843
<<<<<<< HEAD
3944
"id": "d349a99c",
4045
=======
@@ -43,6 +48,9 @@
4348
=======
4449
"id": "de365a2a",
4550
>>>>>>> documentation-devel
51+
=======
52+
"id": "547b0060",
53+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
4654
"metadata": {
4755
"tags": [
4856
"remove_cell"
@@ -61,6 +69,7 @@
6169
"cell_type": "code",
6270
"execution_count": null,
6371
<<<<<<< HEAD
72+
<<<<<<< HEAD
6473
<<<<<<< HEAD
6574
"id": "a273a7b1",
6675
=======
@@ -69,6 +78,9 @@
6978
=======
7079
"id": "8523ec05",
7180
>>>>>>> documentation-devel
81+
=======
82+
"id": "ae22371f",
83+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
7284
"metadata": {
7385
"eval": false,
7486
"tags": [
@@ -110,6 +122,7 @@
110122
"cell_type": "code",
111123
"execution_count": null,
112124
<<<<<<< HEAD
125+
<<<<<<< HEAD
113126
<<<<<<< HEAD
114127
"id": "3a966e13",
115128
=======
@@ -118,6 +131,9 @@
118131
=======
119132
"id": "0f0631ae",
120133
>>>>>>> documentation-devel
134+
=======
135+
"id": "6ec4e401",
136+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
121137
"metadata": {
122138
"lines_to_next_cell": 0,
123139
"name": "setup"
@@ -136,6 +152,7 @@
136152
{
137153
"cell_type": "markdown",
138154
<<<<<<< HEAD
155+
<<<<<<< HEAD
139156
<<<<<<< HEAD
140157
"id": "683d8ba4",
141158
=======
@@ -144,6 +161,9 @@
144161
=======
145162
"id": "7e43bb6d",
146163
>>>>>>> documentation-devel
164+
=======
165+
"id": "916de034",
166+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
147167
"metadata": {},
148168
"source": [
149169
"## Downloading the data\n",
@@ -157,6 +177,7 @@
157177
"cell_type": "code",
158178
"execution_count": null,
159179
<<<<<<< HEAD
180+
<<<<<<< HEAD
160181
<<<<<<< HEAD
161182
"id": "92a66f25",
162183
=======
@@ -165,6 +186,9 @@
165186
=======
166187
"id": "1d7c889b",
167188
>>>>>>> documentation-devel
189+
=======
190+
"id": "b4e548ee",
191+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
168192
"metadata": {
169193
"lines_to_next_cell": 0
170194
},
@@ -177,6 +201,7 @@
177201
{
178202
"cell_type": "markdown",
179203
<<<<<<< HEAD
204+
<<<<<<< HEAD
180205
<<<<<<< HEAD
181206
"id": "6e6baca7",
182207
=======
@@ -185,6 +210,9 @@
185210
=======
186211
"id": "5af2e7d9",
187212
>>>>>>> documentation-devel
213+
=======
214+
"id": "2a4c879c",
215+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
188216
"metadata": {
189217
"lines_to_next_cell": 0
190218
},
@@ -198,6 +226,7 @@
198226
"cell_type": "code",
199227
"execution_count": null,
200228
<<<<<<< HEAD
229+
<<<<<<< HEAD
201230
<<<<<<< HEAD
202231
"id": "d2dbc69d",
203232
=======
@@ -206,6 +235,9 @@
206235
=======
207236
"id": "2014a5c5",
208237
>>>>>>> documentation-devel
238+
=======
239+
"id": "1e3b23f7",
240+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
209241
"metadata": {
210242
"lines_to_next_cell": 0
211243
},
@@ -221,6 +253,7 @@
221253
{
222254
"cell_type": "markdown",
223255
<<<<<<< HEAD
256+
<<<<<<< HEAD
224257
<<<<<<< HEAD
225258
"id": "4d607753",
226259
=======
@@ -229,6 +262,9 @@
229262
=======
230263
"id": "db84994b",
231264
>>>>>>> documentation-devel
265+
=======
266+
"id": "6a702ee2",
267+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
232268
"metadata": {
233269
"lines_to_next_cell": 0
234270
},
@@ -240,6 +276,7 @@
240276
"cell_type": "code",
241277
"execution_count": null,
242278
<<<<<<< HEAD
279+
<<<<<<< HEAD
243280
<<<<<<< HEAD
244281
"id": "761195db",
245282
=======
@@ -248,6 +285,9 @@
248285
=======
249286
"id": "6910b053",
250287
>>>>>>> documentation-devel
288+
=======
289+
"id": "ba21301f",
290+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
251291
"metadata": {
252292
"lines_to_next_cell": 0
253293
},
@@ -261,6 +301,7 @@
261301
{
262302
"cell_type": "markdown",
263303
<<<<<<< HEAD
304+
<<<<<<< HEAD
264305
<<<<<<< HEAD
265306
"id": "78bd2749",
266307
=======
@@ -269,6 +310,9 @@
269310
=======
270311
"id": "c7baabe0",
271312
>>>>>>> documentation-devel
313+
=======
314+
"id": "3cad8cc4",
315+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
272316
"metadata": {
273317
"lines_to_next_cell": 0
274318
},
@@ -281,6 +325,7 @@
281325
"cell_type": "code",
282326
"execution_count": null,
283327
<<<<<<< HEAD
328+
<<<<<<< HEAD
284329
<<<<<<< HEAD
285330
"id": "c4c25f76",
286331
=======
@@ -289,6 +334,9 @@
289334
=======
290335
"id": "17022b20",
291336
>>>>>>> documentation-devel
337+
=======
338+
"id": "5d40495a",
339+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
292340
"metadata": {
293341
"lines_to_next_cell": 0
294342
},
@@ -307,6 +355,7 @@
307355
{
308356
"cell_type": "markdown",
309357
<<<<<<< HEAD
358+
<<<<<<< HEAD
310359
<<<<<<< HEAD
311360
"id": "b82b05b5",
312361
=======
@@ -315,6 +364,9 @@
315364
=======
316365
"id": "7a7ea6b2",
317366
>>>>>>> documentation-devel
367+
=======
368+
"id": "6d309ff1",
369+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
318370
"metadata": {},
319371
"source": [
320372
"Here, spot locations are provided as a CSV file. There are two columns of particular interest, namely `xcoord` and `ycoord`. The barcode column corresponds to the barcodes in the count matrix. Before calling the `SpatialFeatureExperiment` constructor, the spatial coordinates must be converted to a `sf` data frame using `df2sf()`. The coordinates are centroid positions, so we will indicate that `geometryType=\"POINT\"`. "
@@ -324,6 +376,7 @@
324376
"cell_type": "code",
325377
"execution_count": null,
326378
<<<<<<< HEAD
379+
<<<<<<< HEAD
327380
<<<<<<< HEAD
328381
"id": "c8bffe44",
329382
=======
@@ -332,6 +385,9 @@
332385
=======
333386
"id": "1cd10680",
334387
>>>>>>> documentation-devel
388+
=======
389+
"id": "2e1ee07f",
390+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
335391
"metadata": {
336392
"lines_to_next_cell": 0
337393
},
@@ -347,6 +403,7 @@
347403
{
348404
"cell_type": "markdown",
349405
<<<<<<< HEAD
406+
<<<<<<< HEAD
350407
<<<<<<< HEAD
351408
"id": "97430291",
352409
=======
@@ -355,6 +412,9 @@
355412
=======
356413
"id": "534d2b91",
357414
>>>>>>> documentation-devel
415+
=======
416+
"id": "3ca21886",
417+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
358418
"metadata": {
359419
"lines_to_next_cell": 0
360420
},
@@ -366,6 +426,7 @@
366426
"cell_type": "code",
367427
"execution_count": null,
368428
<<<<<<< HEAD
429+
<<<<<<< HEAD
369430
<<<<<<< HEAD
370431
"id": "89a5d0af",
371432
=======
@@ -374,6 +435,9 @@
374435
=======
375436
"id": "870ff045",
376437
>>>>>>> documentation-devel
438+
=======
439+
"id": "87d65336",
440+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
377441
"metadata": {
378442
"lines_to_next_cell": 0
379443
},
@@ -390,6 +454,7 @@
390454
{
391455
"cell_type": "markdown",
392456
<<<<<<< HEAD
457+
<<<<<<< HEAD
393458
<<<<<<< HEAD
394459
"id": "4a1696aa",
395460
=======
@@ -398,6 +463,9 @@
398463
=======
399464
"id": "68756f81",
400465
>>>>>>> documentation-devel
466+
=======
467+
"id": "55be0791",
468+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
401469
"metadata": {
402470
"lines_to_next_cell": 0
403471
},
@@ -409,6 +477,7 @@
409477
"cell_type": "code",
410478
"execution_count": null,
411479
<<<<<<< HEAD
480+
<<<<<<< HEAD
412481
<<<<<<< HEAD
413482
"id": "3951a1be",
414483
=======
@@ -417,6 +486,9 @@
417486
=======
418487
"id": "d74bad63",
419488
>>>>>>> documentation-devel
489+
=======
490+
"id": "28385a6e",
491+
>>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2
420492
"metadata": {},
421493
"outputs": [],
422494
"source": [

0 commit comments

Comments
 (0)