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Merged
LucaMarconato merged 6 commits into from
Apr 4, 2024
Merged

Pass plot notebooks #91

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761fc57
adjust plots aggregation
melonora Apr 1, 2024
0bf8b92
fix plots spatial_query
melonora Apr 1, 2024
0693492
fix cosmx
melonora Apr 1, 2024
1c8faa1
fix visium notebook
melonora Apr 1, 2024
53dfb92
add better explanation polygon_query
melonora Apr 2, 2024
290769d
regenerated notebooks figures
LucaMarconato Apr 4, 2024
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757 changes: 702 additions & 55 deletions notebooks/examples/aggregation.ipynb
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205 changes: 159 additions & 46 deletions notebooks/examples/napari_rois.ipynb
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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,37 +22,15 @@
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" var msg = \"WARNING: it looks like you might have loaded \" +\n",
" \"jupyter_black in a non-lab notebook with \" +\n",
" \"`is_lab=True`. Please double check, and if \" +\n",
" \"loading with `%load_ext` please review the README!\"\n",
" console.log(msg)\n",
" alert(msg)\n",
" })()\n",
" </script>\n",
" "
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"%load_ext jupyter_black"
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]
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Expand All@@ -61,8 +39,8 @@
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Expand DownExpand Up@@ -104,6 +82,10 @@
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Expand DownExpand Up@@ -163,6 +145,10 @@
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Expand DownExpand Up@@ -206,6 +192,10 @@
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Expand DownExpand Up@@ -255,6 +245,10 @@
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Expand DownExpand Up@@ -328,6 +322,10 @@
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Expand All@@ -354,6 +352,10 @@
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Expand DownExpand Up@@ -424,6 +426,10 @@
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Expand DownExpand Up@@ -455,6 +461,10 @@
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Expand DownExpand Up@@ -497,6 +507,10 @@
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Expand DownExpand Up@@ -553,7 +567,12 @@
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"# we rounded the coordinates to make it less verbose here in the notebook\n",
Expand DownExpand Up@@ -592,7 +611,12 @@
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Expand DownExpand Up@@ -641,7 +665,12 @@
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Expand DownExpand Up@@ -671,7 +700,12 @@
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"data": {
Expand DownExpand Up@@ -702,6 +736,69 @@
"filtered_tables"
]
},
{
"cell_type": "markdown",
"id": "b259322b39d43b07",
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"Note that polygon_query only returns a table in case of the table annotating an element in the \n",
"resulting queried `SpatialData` object. Other tables are filtered out. Should you want to keep \n",
"tables that are not annotating any elements in the resulting `SpatialData` object, a parameter \n",
"`filter_tables` set to `False` can be passed on to the `polygon_query` function. Which region(s) or \n",
"elements a table annotates can be retrieved as follows:"
]
},
{
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"id": "7c35473723cb95f3",
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{
"name": "stdout",
"output_type": "stream",
"text": [
"CytAssist_FFPE_Human_Breast_Cancer\n"
]
}
],
"source": [
"from spatialdata import SpatialData\n",
"\n",
"# Note that we could also do visium_sdata.get_annotated regions here. This is just meant to show we\n",
"# can also get annotated regions from a table outside a Spatialdata object.\n",
"print(SpatialData.get_annotated_regions(visium_sdata[\"table\"]))"
]
},
{
"cell_type": "markdown",
"id": "632783dbf2e93b4b",
"metadata": {
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"source": [
"It can be that a table is annotating an element but is still not returned after the polygon query. \n",
"The reason in that case is that the resulting table didn't contain any rows annotating elements in \n",
"the result of the query."
]
},
{
"cell_type": "markdown",
"id": "974e2a73-3296-405b-b57a-3d5199563d10",
Expand All@@ -712,9 +809,13 @@
},
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"id": "e60b1ccb-58a6-4c04-929f-58bfa612fc30",
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"outputs": [],
"source": [
"# it's important for the index to be unique\n",
Expand All@@ -723,9 +824,13 @@
},
{
"cell_type": "code",
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"id": "c8152e43-31db-46e5-a01a-5983960f1910",
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}
},
"outputs": [],
"source": [
"categories = [\"unassigned\"] + list(filtered_tables.keys())\n",
Expand All@@ -740,9 +845,13 @@
},
{
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"id": "460d8932-f73c-4b04-9121-17e2d28779e7",
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}
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{
"data": {
Expand All@@ -755,7 +864,7 @@
"Name: count, dtype: int64"
]
},
"execution_count": 18,
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
Expand All@@ -774,16 +883,20 @@
},
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}
},
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{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING:matplotlib.image:Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
"/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:651: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
"Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
"/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:692: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
" color_vector = color_source_vector.map(color_map)\n"
]
},
Expand Down
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Pass plot notebooks by melonora · Pull Request #91 · scverse/spatialdata-tutorials · GitHub
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Pass plot notebooks#91

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 Merged

LucaMarconato
merged 6 commits into

from

Apr 4, 2024
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Pass plot notebooks
#91
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761fc57

adjust plots aggregation


melonora Apr 1, 2024
0bf8b92

fix plots spatial_query


melonora Apr 1, 2024
0693492

fix cosmx


melonora Apr 1, 2024
1c8faa1

fix visium notebook


melonora Apr 1, 2024
53dfb92

add better explanation polygon_query


melonora Apr 2, 2024
290769d

regenerated notebooks figures


LucaMarconato Apr 4, 2024

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757 changes: 702 additions & 55 deletions
notebooks/examples/aggregation.ipynb

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205 changes: 159 additions & 46 deletions
notebooks/examples/napari_rois.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,37 +22,15 @@
 "cell_type": "code",
 "execution_count": 1,
 "id": "a7943409-b7aa-428b-8fe3-14c76dd2c7ec",
 "metadata": {},
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 {
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 " (function() {\n",
 " if (window.IPython === undefined) {\n",
 " return\n",
 " }\n",
 " var msg = \"WARNING: it looks like you might have loaded \" +\n",
 " \"jupyter_black in a non-lab notebook with \" +\n",
 " \"`is_lab=True`. Please double check, and if \" +\n",
 " \"loading with `%load_ext` please review the README!\"\n",
 " console.log(msg)\n",
 " alert(msg)\n",
 " })()\n",
 " </script>\n",
 " "
 ],
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 },
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 }
 ],
 },
 "outputs": [],
 "source": [
 "%load_ext jupyter_black"
 "# %load_ext jupyter_black"
 ]
 },
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Expand All@@ -61,8 +39,8 @@
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Expand DownExpand Up@@ -104,6 +82,10 @@
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Expand DownExpand Up@@ -163,6 +145,10 @@
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Expand DownExpand Up@@ -206,6 +192,10 @@
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Expand DownExpand Up@@ -255,6 +245,10 @@
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Expand DownExpand Up@@ -328,6 +322,10 @@
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Expand All@@ -354,6 +352,10 @@
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Expand DownExpand Up@@ -424,6 +426,10 @@
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Expand DownExpand Up@@ -455,6 +461,10 @@
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Expand DownExpand Up@@ -497,6 +507,10 @@
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Expand DownExpand Up@@ -553,7 +567,12 @@
 "cell_type": "code",
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 "end_time": "2024-04-02T17:30:49.563825Z",
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 }
 },
 "outputs": [],
 "source": [
 "# we rounded the coordinates to make it less verbose here in the notebook\n",
Expand DownExpand Up@@ -592,7 +611,12 @@
 "cell_type": "code",
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 "id": "a39af193-ecc9-4f2b-9fe3-a21aa6e3612b",
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 "start_time": "2024-04-02T17:30:49.547776500Z"
 }
 },
 "outputs": [
 {
 "data": {
Expand DownExpand Up@@ -641,7 +665,12 @@
 "cell_type": "code",
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 "start_time": "2024-04-02T17:30:49.563825Z"
 }
 },
 "outputs": [
 {
 "name": "stderr",
Expand DownExpand Up@@ -671,7 +700,12 @@
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Expand DownExpand Up@@ -702,6 +736,69 @@
 "filtered_tables"
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 "Note that polygon_query only returns a table in case of the table annotating an element in the \n",
 "resulting queried `SpatialData` object. Other tables are filtered out. Should you want to keep \n",
 "tables that are not annotating any elements in the resulting `SpatialData` object, a parameter \n",
 "`filter_tables` set to `False` can be passed on to the `polygon_query` function. Which region(s) or \n",
 "elements a table annotates can be retrieved as follows:"
 ]
 },
 {
 "cell_type": "code",
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 "id": "7c35473723cb95f3",
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 "text": [
 "CytAssist_FFPE_Human_Breast_Cancer\n"
 ]
 }
 ],
 "source": [
 "from spatialdata import SpatialData\n",
 "\n",
 "# Note that we could also do visium_sdata.get_annotated regions here. This is just meant to show we\n",
 "# can also get annotated regions from a table outside a Spatialdata object.\n",
 "print(SpatialData.get_annotated_regions(visium_sdata[\"table\"]))"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "632783dbf2e93b4b",
 "metadata": {
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 "source": [
 "It can be that a table is annotating an element but is still not returned after the polygon query. \n",
 "The reason in that case is that the resulting table didn't contain any rows annotating elements in \n",
 "the result of the query."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "974e2a73-3296-405b-b57a-3d5199563d10",
Expand All@@ -712,9 +809,13 @@
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 "outputs": [],
 "source": [
 "# it's important for the index to be unique\n",
Expand All@@ -723,9 +824,13 @@
 },
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 "cell_type": "code",
 "execution_count": 17,
 "execution_count": 18,
 "id": "c8152e43-31db-46e5-a01a-5983960f1910",
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 }
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 "source": [
 "categories = [\"unassigned\"] + list(filtered_tables.keys())\n",
Expand All@@ -740,9 +845,13 @@
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Expand All@@ -755,7 +864,7 @@
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Expand All@@ -774,16 +883,20 @@
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 "output_type": "stream",
 "text": [
 "WARNING:matplotlib.image:Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:651: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 "Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:692: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 " color_vector = color_source_vector.map(color_map)\n"
 ]
 },
Expand Down
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Pass plot notebooks by melonora · Pull Request #91 · scverse/spatialdata-tutorials · GitHub
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Pass plot notebooks#91

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 Merged

LucaMarconato
merged 6 commits into

from

Apr 4, 2024
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Pass plot notebooks
#91
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761fc57

adjust plots aggregation


melonora Apr 1, 2024
0bf8b92

fix plots spatial_query


melonora Apr 1, 2024
0693492

fix cosmx


melonora Apr 1, 2024
1c8faa1

fix visium notebook


melonora Apr 1, 2024
53dfb92

add better explanation polygon_query


melonora Apr 2, 2024
290769d

regenerated notebooks figures


LucaMarconato Apr 4, 2024

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757 changes: 702 additions & 55 deletions
notebooks/examples/aggregation.ipynb

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205 changes: 159 additions & 46 deletions
notebooks/examples/napari_rois.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,37 +22,15 @@
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 " var msg = \"WARNING: it looks like you might have loaded \" +\n",
 " \"jupyter_black in a non-lab notebook with \" +\n",
 " \"`is_lab=True`. Please double check, and if \" +\n",
 " \"loading with `%load_ext` please review the README!\"\n",
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 "%load_ext jupyter_black"
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Expand All@@ -61,8 +39,8 @@
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Expand DownExpand Up@@ -104,6 +82,10 @@
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Expand DownExpand Up@@ -163,6 +145,10 @@
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Expand DownExpand Up@@ -206,6 +192,10 @@
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Expand DownExpand Up@@ -255,6 +245,10 @@
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Expand DownExpand Up@@ -328,6 +322,10 @@
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Expand All@@ -354,6 +352,10 @@
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Expand DownExpand Up@@ -424,6 +426,10 @@
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Expand DownExpand Up@@ -455,6 +461,10 @@
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 "id": "265725f6-a143-41e0-8438-9585f4cee09e",
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Expand DownExpand Up@@ -497,6 +507,10 @@
 "execution_count": 11,
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Expand DownExpand Up@@ -553,7 +567,12 @@
 "cell_type": "code",
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 "# we rounded the coordinates to make it less verbose here in the notebook\n",
Expand DownExpand Up@@ -592,7 +611,12 @@
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Expand DownExpand Up@@ -641,7 +665,12 @@
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Expand DownExpand Up@@ -671,7 +700,12 @@
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Expand DownExpand Up@@ -702,6 +736,69 @@
 "filtered_tables"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "b259322b39d43b07",
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 }
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 "source": [
 "Note that polygon_query only returns a table in case of the table annotating an element in the \n",
 "resulting queried `SpatialData` object. Other tables are filtered out. Should you want to keep \n",
 "tables that are not annotating any elements in the resulting `SpatialData` object, a parameter \n",
 "`filter_tables` set to `False` can be passed on to the `polygon_query` function. Which region(s) or \n",
 "elements a table annotates can be retrieved as follows:"
 ]
 },
 {
 "cell_type": "code",
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 "id": "7c35473723cb95f3",
 "metadata": {
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 {
 "name": "stdout",
 "output_type": "stream",
 "text": [
 "CytAssist_FFPE_Human_Breast_Cancer\n"
 ]
 }
 ],
 "source": [
 "from spatialdata import SpatialData\n",
 "\n",
 "# Note that we could also do visium_sdata.get_annotated regions here. This is just meant to show we\n",
 "# can also get annotated regions from a table outside a Spatialdata object.\n",
 "print(SpatialData.get_annotated_regions(visium_sdata[\"table\"]))"
 ]
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 "id": "632783dbf2e93b4b",
 "metadata": {
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 "source": [
 "It can be that a table is annotating an element but is still not returned after the polygon query. \n",
 "The reason in that case is that the resulting table didn't contain any rows annotating elements in \n",
 "the result of the query."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "974e2a73-3296-405b-b57a-3d5199563d10",
Expand All@@ -712,9 +809,13 @@
 },
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 "source": [
 "# it's important for the index to be unique\n",
Expand All@@ -723,9 +824,13 @@
 },
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 "execution_count": 18,
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 "categories = [\"unassigned\"] + list(filtered_tables.keys())\n",
Expand All@@ -740,9 +845,13 @@
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Expand All@@ -755,7 +864,7 @@
 "Name: count, dtype: int64"
 ]
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 "execution_count": 18,
 "execution_count": 19,
 "metadata": {},
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Expand All@@ -774,16 +883,20 @@
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 {
 "name": "stderr",
 "output_type": "stream",
 "text": [
 "WARNING:matplotlib.image:Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:651: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 "Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:692: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 " color_vector = color_source_vector.map(color_map)\n"
 ]
 },
Expand Down
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Pass plot notebooks by melonora · Pull Request #91 · scverse/spatialdata-tutorials · GitHub
Skip to content
Pass plot notebooks#91

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 Merged

LucaMarconato
merged 6 commits into

from

Apr 4, 2024
 Merged


Pass plot notebooks
#91
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761fc57

adjust plots aggregation


melonora Apr 1, 2024
0bf8b92

fix plots spatial_query


melonora Apr 1, 2024
0693492

fix cosmx


melonora Apr 1, 2024
1c8faa1

fix visium notebook


melonora Apr 1, 2024
53dfb92

add better explanation polygon_query


melonora Apr 2, 2024
290769d

regenerated notebooks figures


LucaMarconato Apr 4, 2024

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757 changes: 702 additions & 55 deletions
notebooks/examples/aggregation.ipynb

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205 changes: 159 additions & 46 deletions
notebooks/examples/napari_rois.ipynb

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Expand Up@@ -22,37 +22,15 @@
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Expand DownExpand Up@@ -553,7 +567,12 @@
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Expand DownExpand Up@@ -592,7 +611,12 @@
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Expand DownExpand Up@@ -641,7 +665,12 @@
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Expand DownExpand Up@@ -671,7 +700,12 @@
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Expand DownExpand Up@@ -702,6 +736,69 @@
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 "Note that polygon_query only returns a table in case of the table annotating an element in the \n",
 "resulting queried `SpatialData` object. Other tables are filtered out. Should you want to keep \n",
 "tables that are not annotating any elements in the resulting `SpatialData` object, a parameter \n",
 "`filter_tables` set to `False` can be passed on to the `polygon_query` function. Which region(s) or \n",
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 "# Note that we could also do visium_sdata.get_annotated regions here. This is just meant to show we\n",
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Expand All@@ -712,9 +809,13 @@
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 "# it's important for the index to be unique\n",
Expand All@@ -723,9 +824,13 @@
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Expand All@@ -740,9 +845,13 @@
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Expand All@@ -755,7 +864,7 @@
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 "WARNING:matplotlib.image:Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:651: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
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 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:692: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
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Pass plot notebooks by melonora · Pull Request #91 · scverse/spatialdata-tutorials · GitHub
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 Merged

LucaMarconato
merged 6 commits into

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Apr 4, 2024
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Pass plot notebooks
#91
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761fc57

adjust plots aggregation


melonora Apr 1, 2024
0bf8b92

fix plots spatial_query


melonora Apr 1, 2024
0693492

fix cosmx


melonora Apr 1, 2024
1c8faa1

fix visium notebook


melonora Apr 1, 2024
53dfb92

add better explanation polygon_query


melonora Apr 2, 2024
290769d

regenerated notebooks figures


LucaMarconato Apr 4, 2024

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757 changes: 702 additions & 55 deletions
notebooks/examples/aggregation.ipynb

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205 changes: 159 additions & 46 deletions
notebooks/examples/napari_rois.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,37 +22,15 @@
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Expand All@@ -61,8 +39,8 @@
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Expand DownExpand Up@@ -104,6 +82,10 @@
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Expand DownExpand Up@@ -163,6 +145,10 @@
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Expand DownExpand Up@@ -206,6 +192,10 @@
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Expand DownExpand Up@@ -255,6 +245,10 @@
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Expand DownExpand Up@@ -328,6 +322,10 @@
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Expand All@@ -354,6 +352,10 @@
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Expand DownExpand Up@@ -424,6 +426,10 @@
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Expand DownExpand Up@@ -455,6 +461,10 @@
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Expand DownExpand Up@@ -497,6 +507,10 @@
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Expand DownExpand Up@@ -553,7 +567,12 @@
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 "# we rounded the coordinates to make it less verbose here in the notebook\n",
Expand DownExpand Up@@ -592,7 +611,12 @@
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Expand DownExpand Up@@ -641,7 +665,12 @@
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Expand DownExpand Up@@ -671,7 +700,12 @@
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Expand DownExpand Up@@ -702,6 +736,69 @@
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 "resulting queried `SpatialData` object. Other tables are filtered out. Should you want to keep \n",
 "tables that are not annotating any elements in the resulting `SpatialData` object, a parameter \n",
 "`filter_tables` set to `False` can be passed on to the `polygon_query` function. Which region(s) or \n",
 "elements a table annotates can be retrieved as follows:"
 ]
 },
 {
 "cell_type": "code",
 "execution_count": 16,
 "id": "7c35473723cb95f3",
 "metadata": {
 "ExecuteTime": {
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 "text": [
 "CytAssist_FFPE_Human_Breast_Cancer\n"
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 }
 ],
 "source": [
 "from spatialdata import SpatialData\n",
 "\n",
 "# Note that we could also do visium_sdata.get_annotated regions here. This is just meant to show we\n",
 "# can also get annotated regions from a table outside a Spatialdata object.\n",
 "print(SpatialData.get_annotated_regions(visium_sdata[\"table\"]))"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "632783dbf2e93b4b",
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 "It can be that a table is annotating an element but is still not returned after the polygon query. \n",
 "The reason in that case is that the resulting table didn't contain any rows annotating elements in \n",
 "the result of the query."
 ]
 },
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Expand All@@ -712,9 +809,13 @@
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 "# it's important for the index to be unique\n",
Expand All@@ -723,9 +824,13 @@
 },
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 "id": "c8152e43-31db-46e5-a01a-5983960f1910",
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 "categories = [\"unassigned\"] + list(filtered_tables.keys())\n",
Expand All@@ -740,9 +845,13 @@
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Expand All@@ -755,7 +864,7 @@
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Expand All@@ -774,16 +883,20 @@
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 "WARNING:matplotlib.image:Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
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 "Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:692: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 " color_vector = color_source_vector.map(color_map)\n"
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 },
Expand Down
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Pass plot notebooks by melonora · Pull Request #91 · scverse/spatialdata-tutorials · GitHub
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Pass plot notebooks#91

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 Merged

LucaMarconato
merged 6 commits into

from

Apr 4, 2024
 Merged


Pass plot notebooks
#91
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761fc57

adjust plots aggregation


melonora Apr 1, 2024
0bf8b92

fix plots spatial_query


melonora Apr 1, 2024
0693492

fix cosmx


melonora Apr 1, 2024
1c8faa1

fix visium notebook


melonora Apr 1, 2024
53dfb92

add better explanation polygon_query


melonora Apr 2, 2024
290769d

regenerated notebooks figures


LucaMarconato Apr 4, 2024

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757 changes: 702 additions & 55 deletions
notebooks/examples/aggregation.ipynb

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205 changes: 159 additions & 46 deletions
notebooks/examples/napari_rois.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,37 +22,15 @@
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 " \"jupyter_black in a non-lab notebook with \" +\n",
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Expand All@@ -61,8 +39,8 @@
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Expand DownExpand Up@@ -104,6 +82,10 @@
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Expand DownExpand Up@@ -163,6 +145,10 @@
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Expand DownExpand Up@@ -206,6 +192,10 @@
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Expand DownExpand Up@@ -255,6 +245,10 @@
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Expand DownExpand Up@@ -328,6 +322,10 @@
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Expand All@@ -354,6 +352,10 @@
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Expand DownExpand Up@@ -424,6 +426,10 @@
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Expand DownExpand Up@@ -455,6 +461,10 @@
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Expand DownExpand Up@@ -497,6 +507,10 @@
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Expand DownExpand Up@@ -553,7 +567,12 @@
 "cell_type": "code",
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 "# we rounded the coordinates to make it less verbose here in the notebook\n",
Expand DownExpand Up@@ -592,7 +611,12 @@
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Expand DownExpand Up@@ -641,7 +665,12 @@
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Expand DownExpand Up@@ -671,7 +700,12 @@
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Expand DownExpand Up@@ -702,6 +736,69 @@
 "filtered_tables"
 ]
 },
 {
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 "id": "b259322b39d43b07",
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 }
 },
 "source": [
 "Note that polygon_query only returns a table in case of the table annotating an element in the \n",
 "resulting queried `SpatialData` object. Other tables are filtered out. Should you want to keep \n",
 "tables that are not annotating any elements in the resulting `SpatialData` object, a parameter \n",
 "`filter_tables` set to `False` can be passed on to the `polygon_query` function. Which region(s) or \n",
 "elements a table annotates can be retrieved as follows:"
 ]
 },
 {
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 "id": "7c35473723cb95f3",
 "metadata": {
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 "outputs": [
 {
 "name": "stdout",
 "output_type": "stream",
 "text": [
 "CytAssist_FFPE_Human_Breast_Cancer\n"
 ]
 }
 ],
 "source": [
 "from spatialdata import SpatialData\n",
 "\n",
 "# Note that we could also do visium_sdata.get_annotated regions here. This is just meant to show we\n",
 "# can also get annotated regions from a table outside a Spatialdata object.\n",
 "print(SpatialData.get_annotated_regions(visium_sdata[\"table\"]))"
 ]
 },
 {
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 "id": "632783dbf2e93b4b",
 "metadata": {
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 "source": [
 "It can be that a table is annotating an element but is still not returned after the polygon query. \n",
 "The reason in that case is that the resulting table didn't contain any rows annotating elements in \n",
 "the result of the query."
 ]
 },
 {
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 "id": "974e2a73-3296-405b-b57a-3d5199563d10",
Expand All@@ -712,9 +809,13 @@
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 "source": [
 "# it's important for the index to be unique\n",
Expand All@@ -723,9 +824,13 @@
 },
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 "cell_type": "code",
 "execution_count": 17,
 "execution_count": 18,
 "id": "c8152e43-31db-46e5-a01a-5983960f1910",
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 "categories = [\"unassigned\"] + list(filtered_tables.keys())\n",
Expand All@@ -740,9 +845,13 @@
 },
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Expand All@@ -755,7 +864,7 @@
 "Name: count, dtype: int64"
 ]
 },
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Expand All@@ -774,16 +883,20 @@
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 }
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 "name": "stderr",
 "output_type": "stream",
 "text": [
 "WARNING:matplotlib.image:Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:651: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 "Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:692: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 " color_vector = color_source_vector.map(color_map)\n"
 ]
 },
Expand Down
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Pass plot notebooks by melonora · Pull Request #91 · scverse/spatialdata-tutorials · GitHub
Skip to content
Pass plot notebooks#91

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 Merged

LucaMarconato
merged 6 commits into

from

Apr 4, 2024
 Merged


Pass plot notebooks
#91
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761fc57

adjust plots aggregation


melonora Apr 1, 2024
0bf8b92

fix plots spatial_query


melonora Apr 1, 2024
0693492

fix cosmx


melonora Apr 1, 2024
1c8faa1

fix visium notebook


melonora Apr 1, 2024
53dfb92

add better explanation polygon_query


melonora Apr 2, 2024
290769d

regenerated notebooks figures


LucaMarconato Apr 4, 2024

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757 changes: 702 additions & 55 deletions
notebooks/examples/aggregation.ipynb

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205 changes: 159 additions & 46 deletions
notebooks/examples/napari_rois.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,37 +22,15 @@
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 " var msg = \"WARNING: it looks like you might have loaded \" +\n",
 " \"jupyter_black in a non-lab notebook with \" +\n",
 " \"`is_lab=True`. Please double check, and if \" +\n",
 " \"loading with `%load_ext` please review the README!\"\n",
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Expand All@@ -61,8 +39,8 @@
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Expand DownExpand Up@@ -104,6 +82,10 @@
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Expand DownExpand Up@@ -163,6 +145,10 @@
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Expand DownExpand Up@@ -206,6 +192,10 @@
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Expand DownExpand Up@@ -255,6 +245,10 @@
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Expand DownExpand Up@@ -328,6 +322,10 @@
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Expand All@@ -354,6 +352,10 @@
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Expand DownExpand Up@@ -424,6 +426,10 @@
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Expand DownExpand Up@@ -455,6 +461,10 @@
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Expand DownExpand Up@@ -497,6 +507,10 @@
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Expand DownExpand Up@@ -553,7 +567,12 @@
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 "# we rounded the coordinates to make it less verbose here in the notebook\n",
Expand DownExpand Up@@ -592,7 +611,12 @@
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Expand DownExpand Up@@ -641,7 +665,12 @@
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Expand DownExpand Up@@ -671,7 +700,12 @@
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Expand DownExpand Up@@ -702,6 +736,69 @@
 "filtered_tables"
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 {
 "cell_type": "markdown",
 "id": "b259322b39d43b07",
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 "source": [
 "Note that polygon_query only returns a table in case of the table annotating an element in the \n",
 "resulting queried `SpatialData` object. Other tables are filtered out. Should you want to keep \n",
 "tables that are not annotating any elements in the resulting `SpatialData` object, a parameter \n",
 "`filter_tables` set to `False` can be passed on to the `polygon_query` function. Which region(s) or \n",
 "elements a table annotates can be retrieved as follows:"
 ]
 },
 {
 "cell_type": "code",
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 "id": "7c35473723cb95f3",
 "metadata": {
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 "name": "stdout",
 "output_type": "stream",
 "text": [
 "CytAssist_FFPE_Human_Breast_Cancer\n"
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 }
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 "source": [
 "from spatialdata import SpatialData\n",
 "\n",
 "# Note that we could also do visium_sdata.get_annotated regions here. This is just meant to show we\n",
 "# can also get annotated regions from a table outside a Spatialdata object.\n",
 "print(SpatialData.get_annotated_regions(visium_sdata[\"table\"]))"
 ]
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 {
 "cell_type": "markdown",
 "id": "632783dbf2e93b4b",
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 "source": [
 "It can be that a table is annotating an element but is still not returned after the polygon query. \n",
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 "the result of the query."
 ]
 },
 {
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 "id": "974e2a73-3296-405b-b57a-3d5199563d10",
Expand All@@ -712,9 +809,13 @@
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 }
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 "outputs": [],
 "source": [
 "# it's important for the index to be unique\n",
Expand All@@ -723,9 +824,13 @@
 },
 {
 "cell_type": "code",
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 "execution_count": 18,
 "id": "c8152e43-31db-46e5-a01a-5983960f1910",
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 "metadata": {
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 "outputs": [],
 "source": [
 "categories = [\"unassigned\"] + list(filtered_tables.keys())\n",
Expand All@@ -740,9 +845,13 @@
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Expand All@@ -755,7 +864,7 @@
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Expand All@@ -774,16 +883,20 @@
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 "text": [
 "WARNING:matplotlib.image:Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:651: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 "Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:692: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
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 },
Expand Down
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Pass plot notebooks by melonora · Pull Request #91 · scverse/spatialdata-tutorials · GitHub
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 Merged

LucaMarconato
merged 6 commits into

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Apr 4, 2024
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Pass plot notebooks
#91
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761fc57

adjust plots aggregation


melonora Apr 1, 2024
0bf8b92

fix plots spatial_query


melonora Apr 1, 2024
0693492

fix cosmx


melonora Apr 1, 2024
1c8faa1

fix visium notebook


melonora Apr 1, 2024
53dfb92

add better explanation polygon_query


melonora Apr 2, 2024
290769d

regenerated notebooks figures


LucaMarconato Apr 4, 2024

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757 changes: 702 additions & 55 deletions
notebooks/examples/aggregation.ipynb

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205 changes: 159 additions & 46 deletions
notebooks/examples/napari_rois.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,37 +22,15 @@
 "cell_type": "code",
 "execution_count": 1,
 "id": "a7943409-b7aa-428b-8fe3-14c76dd2c7ec",
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 {
 "data": {
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 " \"jupyter_black in a non-lab notebook with \" +\n",
 " \"`is_lab=True`. Please double check, and if \" +\n",
 " \"loading with `%load_ext` please review the README!\"\n",
 " console.log(msg)\n",
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 "outputs": [],
 "source": [
 "%load_ext jupyter_black"
 "# %load_ext jupyter_black"
 ]
 },
 {
Expand All@@ -61,8 +39,8 @@
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Expand DownExpand Up@@ -104,6 +82,10 @@
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Expand DownExpand Up@@ -163,6 +145,10 @@
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Expand DownExpand Up@@ -206,6 +192,10 @@
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Expand DownExpand Up@@ -255,6 +245,10 @@
 "execution_count": 6,
 "id": "7eb48cd4-8093-4262-885b-16229a3ec51f",
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Expand DownExpand Up@@ -328,6 +322,10 @@
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Expand All@@ -354,6 +352,10 @@
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Expand DownExpand Up@@ -424,6 +426,10 @@
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Expand DownExpand Up@@ -455,6 +461,10 @@
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Expand DownExpand Up@@ -497,6 +507,10 @@
 "execution_count": 11,
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Expand DownExpand Up@@ -553,7 +567,12 @@
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 "# we rounded the coordinates to make it less verbose here in the notebook\n",
Expand DownExpand Up@@ -592,7 +611,12 @@
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Expand DownExpand Up@@ -641,7 +665,12 @@
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Expand DownExpand Up@@ -671,7 +700,12 @@
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Expand DownExpand Up@@ -702,6 +736,69 @@
 "filtered_tables"
 ]
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 "Note that polygon_query only returns a table in case of the table annotating an element in the \n",
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 "`filter_tables` set to `False` can be passed on to the `polygon_query` function. Which region(s) or \n",
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 "metadata": {
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 "from spatialdata import SpatialData\n",
 "\n",
 "# Note that we could also do visium_sdata.get_annotated regions here. This is just meant to show we\n",
 "# can also get annotated regions from a table outside a Spatialdata object.\n",
 "print(SpatialData.get_annotated_regions(visium_sdata[\"table\"]))"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "632783dbf2e93b4b",
 "metadata": {
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 }
 },
 "source": [
 "It can be that a table is annotating an element but is still not returned after the polygon query. \n",
 "The reason in that case is that the resulting table didn't contain any rows annotating elements in \n",
 "the result of the query."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "974e2a73-3296-405b-b57a-3d5199563d10",
Expand All@@ -712,9 +809,13 @@
 },
 {
 "cell_type": "code",
 "execution_count": 16,
 "execution_count": 17,
 "id": "e60b1ccb-58a6-4c04-929f-58bfa612fc30",
 "metadata": {},
 "metadata": {
 "ExecuteTime": {
 "start_time": "2024-04-02T17:30:50.181187Z"
 }
 },
 "outputs": [],
 "source": [
 "# it's important for the index to be unique\n",
Expand All@@ -723,9 +824,13 @@
 },
 {
 "cell_type": "code",
 "execution_count": 17,
 "execution_count": 18,
 "id": "c8152e43-31db-46e5-a01a-5983960f1910",
 "metadata": {},
 "metadata": {
 "ExecuteTime": {
 "start_time": "2024-04-02T17:30:50.182187500Z"
 }
 },
 "outputs": [],
 "source": [
 "categories = [\"unassigned\"] + list(filtered_tables.keys())\n",
Expand All@@ -740,9 +845,13 @@
 },
 {
 "cell_type": "code",
 "execution_count": 18,
 "execution_count": 19,
 "id": "460d8932-f73c-4b04-9121-17e2d28779e7",
 "metadata": {},
 "metadata": {
 "ExecuteTime": {
 "start_time": "2024-04-02T17:30:50.183187300Z"
 }
 },
 "outputs": [
 {
 "data": {
Expand All@@ -755,7 +864,7 @@
 "Name: count, dtype: int64"
 ]
 },
 "execution_count": 18,
 "execution_count": 19,
 "metadata": {},
 "output_type": "execute_result"
 }
Expand All@@ -774,16 +883,20 @@
 },
 {
 "cell_type": "code",
 "execution_count": 19,
 "execution_count": 20,
 "id": "28ebf11b-b070-4b7a-8651-02affa387b6c",
 "metadata": {},
 "metadata": {
 "ExecuteTime": {
 "start_time": "2024-04-02T17:30:50.184187400Z"
 }
 },
 "outputs": [
 {
 "name": "stderr",
 "output_type": "stream",
 "text": [
 "WARNING:matplotlib.image:Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:651: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 "Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).\n",
 "/Users/macbook/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:692: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning\n",
 " color_vector = color_source_vector.map(color_map)\n"
 ]
 },
Expand Down
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