AnnData _repr_html_ Visual Test

This page displays various AnnData configurations to visually verify the HTML representation.

1. Full AnnData (all features)

AnnData 100 obs × 50 vars
obs_names: 0, 1, 2, 3, 4, ..., 95, 96, 97, 98, 99
var_names: 0, 1, 2, 3, 4, ..., 45, 46, 47, 48, 49
X csr_matrix (100 × 50) float32 · 90.0% sparse (500 stored)
obs (5 columns) ?
batch
 category (2) AB
n_counts
 int64 (100 unique)
cell_type
 category (3) B cellNK cellT cell
string_col
 str (!) (5 unique)
donor_id
 str (100 unique)
var (3 columns) ?
gene_name
 str (50 unique)
highly_variable
 bool (2 unique)
mean_expression
 float32 (50 unique)
uns (11 items) ?
batch_colors
 colors (2)
cell_type_colors
 colors (3)
mismatched_colors
 colors (1)
nested_adata
 AnnData (10 × 5)
AnnData 10 obs × 5 vars
X ndarray (10 × 5) float64
obs (1 columns) ?
inner_col
 int64 (10 unique)
var (empty) ?
No entries
uns (empty) ?
No entries
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
neighbors
 dict {params}
pca
 dict {variance, variance_ratio}
string_value
 str "This is a test string"
int_value
 int 42
float_value
 float 3.14159
list_value
 list (5 items)
unserializable
 CustomClass (!)
obsm (4 items) ?
X_pca
 ndarray (100 × 50) float32 (50 cols)
X_umap
 ndarray (100 × 2) float32 (2 cols)
X_tsne
 ndarray (100 × 2) float32 (2 cols)
cell_metadata
 DataFrame (100 × 3) [spatial_x, spatial_y, area]
varm (1 items) ?
PCs
 ndarray (50 × 50) float32 (50 cols)
layers (2 items) ?
raw
 csr_matrix (100 × 50) float64
normalized
 ndarray (100 × 50) float32
obsp (2 items) ?
distances
 csr_matrix (100 × 100) float64
connectivities
 csr_matrix (100 × 100) float64
varp (1 items) ?
gene_corr
 csr_matrix (50 × 50) float64
anndata v0.13.0.dev115+g6f5e2223e ~89.6 KB

2. Empty AnnData

AnnData 0 obs × 0 vars
obs_names: empty
var_names: empty
X None
obs (empty) ?
No entries
var (empty) ?
No entries
uns (empty) ?
No entries
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~16 B

3. Minimal AnnData (just X matrix)

AnnData 10 obs × 5 vars
obs_names: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
var_names: 0, 1, 2, 3, 4
X ndarray (10 × 5) float64
obs (empty) ?
No entries
var (empty) ?
No entries
uns (empty) ?
No entries
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~663 B

4. AnnData View (subset)

AnnData 20 obs × 10 vars View
obs_names: 0, 1, 2, 3, 4, ..., 15, 16, 17, 18, 19
var_names: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
X csr_matrix (20 × 10) float32 · 90.0% sparse (20 stored)
obs (5 columns) ?
batch
 category (2) AB
n_counts
 int64 (20 unique)
cell_type
 category (3) B cellNK cellT cell
string_col
 str (!) (5 unique)
donor_id
 str (20 unique)
var (3 columns) ?
gene_name
 str (10 unique)
highly_variable
 bool (2 unique)
mean_expression
 float32 (10 unique)
uns (11 items) ?
batch_colors
 colors (2)
cell_type_colors
 colors (3)
mismatched_colors
 colors (1)
nested_adata
 AnnData (10 × 5)
AnnData 10 obs × 5 vars
X ndarray (10 × 5) float64
obs (1 columns) ?
inner_col
 int64 (10 unique)
var (empty) ?
No entries
uns (empty) ?
No entries
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
neighbors
 dict {params}
pca
 dict {variance, variance_ratio}
string_value
 str "This is a test string"
int_value
 int 42
float_value
 float 3.14159
list_value
 list (5 items)
unserializable
 CustomClass (!)
obsm (4 items) ?
X_pca
 ndarray (20 × 50) float32 (50 cols)
X_umap
 ndarray (20 × 2) float32 (2 cols)
X_tsne
 ndarray (20 × 2) float32 (2 cols)
cell_metadata
 DataFrame (20 × 3) [spatial_x, spatial_y, area]
varm (1 items) ?
PCs
 ndarray (10 × 50) float32 (50 cols)
layers (2 items) ?
raw
 csr_matrix (20 × 10) float64
normalized
 ndarray (20 × 10) float32
obsp (2 items) ?
distances
 csr_matrix (20 × 20) float64
connectivities
 csr_matrix (20 × 20) float64
varp (1 items) ?
gene_corr
 csr_matrix (10 × 10) float64
anndata v0.13.0.dev115+g6f5e2223e

5. Dense Matrix with Categories

AnnData 50 obs × 30 vars
obs_names: 0, 1, 2, 3, 4, ..., 45, 46, 47, 48, 49
var_names: 0, 1, 2, 3, 4, ..., 25, 26, 27, 28, 29
X ndarray (50 × 30) float32
obs (1 columns) ?
cluster
 category (5) ABCDE
var (empty) ?
No entries
uns (1 items) ?
cluster_colors
 colors (5)
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~9.0 KB

6. Many Columns (tests auto-folding)

AnnData 20 obs × 10 vars
obs_names: 0, 1, 2, 3, 4, ..., 15, 16, 17, 18, 19
var_names: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
X ndarray (20 × 10) float64
obs (15 columns) ?
column_0
 int64 (20 unique)
column_1
 int64 (20 unique)
column_2
 int64 (20 unique)
column_3
 int64 (20 unique)
column_4
 int64 (20 unique)
column_5
 int64 (20 unique)
column_6
 int64 (20 unique)
column_7
 int64 (20 unique)
column_8
 int64 (20 unique)
column_9
 int64 (20 unique)
column_10
 int64 (20 unique)
column_11
 int64 (20 unique)
column_12
 int64 (20 unique)
column_13
 int64 (20 unique)
column_14
 int64 (20 unique)
var (empty) ?
No entries
uns (empty) ?
No entries
obsm (12 items) ?
X_embedding_0
 ndarray (20 × 2) float32 (2 cols)
X_embedding_1
 ndarray (20 × 2) float32 (2 cols)
X_embedding_2
 ndarray (20 × 2) float32 (2 cols)
X_embedding_3
 ndarray (20 × 2) float32 (2 cols)
X_embedding_4
 ndarray (20 × 2) float32 (2 cols)
X_embedding_5
 ndarray (20 × 2) float32 (2 cols)
X_embedding_6
 ndarray (20 × 2) float32 (2 cols)
X_embedding_7
 ndarray (20 × 2) float32 (2 cols)
X_embedding_8
 ndarray (20 × 2) float32 (2 cols)
X_embedding_9
 ndarray (20 × 2) float32 (2 cols)
X_embedding_10
 ndarray (20 × 2) float32 (2 cols)
X_embedding_11
 ndarray (20 × 2) float32 (2 cols)
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~8.2 KB

7. Special Characters (XSS/Unicode test)

AnnData 5 obs × 3 vars
obs_names: 0, 1, 2, 3, 4
var_names: 0, 1, 2
X ndarray (5 × 3) float64
obs (2 columns) ?
column<with>html
 int64 (5 unique)
column&ampersand
 int64 (5 unique)
var (empty) ?
No entries
uns (2 items) ?
key"with'quotes
 str "value"
unicode_日本語
 str "japanese"
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~667 B

8. Dask Array (lazy/chunked)

AnnData 100 obs × 50 vars
obs_names: 0, 1, 2, 3, 4, ..., 95, 96, 97, 98, 99
var_names: 0, 1, 2, 3, 4, ..., 45, 46, 47, 48, 49
X dask.array (100 × 50) float64 · chunks=((10, 10, 10, 10, 10, 10, 10, 10, 10, 10), (50,))
obs (empty) ?
No entries
var (empty) ?
No entries
uns (empty) ?
No entries
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~1.5 KB

9. Backed AnnData (H5AD file)

File path: /var/folders/h_/5f32jgps7yq4np44vpfbx4300000gn/T/tmpz4u4d34u.h5ad. Shows badge with format and status, plus file path.
AnnData 50 obs × 20 vars H5AD (Open) /var/folders/h_/5f32jgps7yq4np44vpfbx4300000gn/T/tmpz4u4d34u.h5ad
obs_names: 0, 1, 2, 3, 4, ..., 45, 46, 47, 48, 49
var_names: 0, 1, 2, 3, 4, ..., 15, 16, 17, 18, 19
X Dataset (50 × 20) float32 · on disk
obs (1 columns) ?
cluster
 category (3) ABC
var (1 columns) ?
gene_name
 str (20 unique)
uns (empty) ?
No entries
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~3.6 KB

10. Deeply Nested AnnData (tests max depth)

AnnData 20 obs × 10 vars
obs_names: 0, 1, 2, 3, 4, ..., 15, 16, 17, 18, 19
var_names: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
X ndarray (20 × 10) float64
obs (empty) ?
No entries
var (empty) ?
No entries
uns (1 items) ?
level1
 AnnData (10 × 5)
AnnData 10 obs × 5 vars
X ndarray (10 × 5) float64
obs (empty) ?
No entries
var (empty) ?
No entries
uns (1 items) ?
level2
 AnnData (5 × 3)
AnnData 5 obs × 3 vars
X ndarray (5 × 3) float64
obs (empty) ?
No entries
var (empty) ?
No entries
uns (1 items) ?
level3
 AnnData (3 × 2)
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~3.1 KB

11. Many Categories (tests truncation)

Default max_categories is 100; set to 20 here to test truncation. cell_type has 30 categories (shows 20 + '...+10'). Click ⋯ button to expand.
AnnData 100 obs × 10 vars
obs_names: 0, 1, 2, 3, 4, ..., 95, 96, 97, 98, 99
var_names: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
X ndarray (100 × 10) float64
obs (2 columns) ?
cell_type
 category (30) type_0type_1type_10type_11type_12type_13type_14type_15type_16type_17type_18type_19type_2type_20type_21type_22type_23type_24type_25type_26...+10
batch
 category (20) batch_0batch_1batch_10batch_11batch_12batch_13batch_14batch_15batch_16batch_17batch_18batch_19batch_2batch_3batch_4batch_5batch_6batch_7batch_8batch_9
var (empty) ?
No entries
uns (2 items) ?
cell_type_colors
 colors (30) +15
batch_colors
 colors (20) +5
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~14.5 KB

12. Uns Value Previews and Type Hints

Shows: (1) preview values for simple types, (2) 'analysis_history' with registered TypeFormatter (shows '3 runs · params: method=umap...'), (3) unregistered type hints show 'import X to enable' message.
AnnData 10 obs × 5 vars
obs_names: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
var_names: 0, 1, 2, 3, 4
X ndarray (10 × 5) float64
obs (empty) ?
No entries
var (empty) ?
No entries
uns (12 items) ?
string_param
 str "A short string value"
long_string
 str "This is a very long string that should be truncated in the preview because it exceeds the maximum le..."
int_param
 int 42
float_param
 float 3.14159
bool_param
 bool True
none_param
 NoneType None
small_list
 list [1, 2, 3]
small_dict
 dict {a, b}
larger_dict
 dict {key1, key2, ...} (5 keys)
analysis_history
 analysis history
3 runs · params: method=umap, n_neighbors=15, metric=euclidean
unregistered_data
 dict [otherpackage.custom_type] (import otherpackage to enable) {data}
string_hint
 str [otherpackage.config] (import otherpackage to enable) "{'setting': 'value'}"
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~1.8 KB

13. No JavaScript (graceful degradation)

This example has script tags removed to simulate environments where JS is disabled. All content should be visible, sections should be expanded, category lists and DataFrame column lists should wrap naturally to multiple lines, and interactive buttons (fold icons, copy buttons, search, expand, wrap toggle) should be hidden. The obsm 'cell_measurements' DataFrame has 20 columns to test column list wrapping.
AnnData 30 obs × 15 vars
obs_names: 0, 1, 2, 3, 4, ..., 25, 26, 27, 28, 29
var_names: 0, 1, 2, 3, 4, ..., 10, 11, 12, 13, 14
X ndarray (30 × 15) float32
obs (9 columns) ?
group
 category (3) XYZ
metric_0
 float64 (30 unique)
metric_1
 float64 (30 unique)
metric_2
 float64 (30 unique)
metric_3
 float64 (30 unique)
metric_4
 float64 (30 unique)
metric_5
 float64 (30 unique)
metric_6
 float64 (30 unique)
metric_7
 float64 (30 unique)
var (empty) ?
No entries
uns (1 items) ?
group_colors
 colors (3)
obsm (2 items) ?
X_pca
 ndarray (30 × 10) float32 (10 cols)
cell_measurements
 DataFrame (30 × 20) [area, perimeter, circularity, eccentricity, solidity, extent, major_axis_length, minor_axis_length, orientation, mean_intensity, max_intensity, min_intensity, std_intensity, centroid_x, centroid_y, bbox_area, convex_area, euler_number, equivalent_diameter, filled_area]
varm (empty) ?
No entries
layers (1 items) ?
raw
 ndarray (30 × 15) float32
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~14.5 KB

14. Custom Sections (TreeData example)

Demonstrates how to add custom sections using SectionFormatter. This example uses TreeData to show 'obst' and 'vart' sections (scverse ecosystem PR). The 'obst' section appears after 'obsm' and 'vart' after 'varm'. Click the expand button (▸) to see an SVG tree visualization. Trees with >30 leaves show a text message instead of the full preview.
TreeData 24 obs × 45 vars TreeData
obs_names: cell_0, cell_1, cell_2, cell_3, cell_4, ..., cell_19, cell_20, cell_21, cell_22, cell_23
var_names: gene_0, gene_1, gene_2, gene_3, gene_4, ..., gene_40, gene_41, gene_42, gene_43, gene_44
X ndarray (24 × 45) float32
obs (1 columns) ?
cell_type
 category (2) B cellT cell
var (1 columns) ?
gene_name
 str (45 unique)
uns (1 items) ?
cell_type_colors
 colors (2)
obsm (1 items) ?
X_pca
 ndarray (24 × 10) float32 (10 cols)
obst (1 items) ?
phylogeny
 DiGraph (31 nodes, 24 leaves)
varm (empty) ?
No entries
vart (1 items) ?
gene_ontology
 DiGraph (54 nodes, 45 leaves)
Tree with 45 leaves (too large to preview)
layers (1 items) ?
raw
 ndarray (24 × 45) float32
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~13.1 KB

15. Expandable DataFrame in obsm

When anndata.settings.repr_html_dataframe_expand = True, DataFrames in obsm/varm show an 'Expand' button. Click to see pandas _repr_html_() output (styled table with zebra striping and hover). Configure pandas display options: pd.set_option('display.max_rows', 10). Column names are shown in the rightmost column (meta column).
AnnData 30 obs × 10 vars
obs_names: 0, 1, 2, 3, 4, ..., 25, 26, 27, 28, 29
var_names: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
X ndarray (30 × 10) float32
obs (1 columns) ?
group
 category (3) ABC
var (empty) ?
No entries
uns (empty) ?
No entries
obsm (2 items) ?
spatial_metrics
 DataFrame (30 × 12) [x_centroid, y_centroid, area, perimeter, circularity, eccentricity, solidity, extent, major_axis, minor_axis, orientation, intensity_mean]
x_centroid y_centroid area perimeter circularity eccentricity solidity extent major_axis minor_axis orientation intensity_mean
0 38.680852 123.087451 431.498416 97.307680 0.273640 0.453990 0.556785 0.487265 8.674803 22.172009 119.144454 152.000899
1 109.098043 168.501428 443.046718 75.929251 0.487834 0.762447 0.845121 0.429985 18.987576 8.323940 135.211885 110.630200
2 201.227045 56.288086 98.326792 96.776147 0.082272 0.126002 0.795926 0.596911 40.072289 8.448481 135.696255 41.923410
3 102.370955 -87.981435 368.713043 43.974049 0.459584 0.196419 0.175123 0.999558 19.604679 28.900810 104.020400 29.728684
4 24.930860 198.706111 143.259774 27.836848 0.306463 0.951445 0.672765 0.769449 37.538482 0.308535 162.784759 139.407399
5 104.508847 -53.097090 401.320156 79.829320 0.822381 0.175492 0.220504 0.397866 6.274315 21.481499 147.133413 230.115323
6 14.488783 -33.513778 498.618950 32.625392 0.056979 0.567727 0.218208 0.827553 38.638571 21.187385 136.268661 87.709210
7 2.390304 34.233783 15.013003 29.938337 0.418607 0.579314 0.874072 0.170708 11.846666 18.680686 10.008994 186.915027
8 -35.141424 155.416042 448.682933 23.250599 0.458431 0.489624 0.249669 0.030464 33.869656 29.703265 1.238033 167.958646
9 156.341336 85.397598 311.315267 12.967898 0.725006 0.644745 0.263247 0.204448 28.289078 9.356383 38.240510 237.546503
10 -81.842867 41.486550 486.691310 25.646306 0.574288 0.229827 0.000653 0.340412 46.457236 10.199156 119.434247 209.350159
11 153.236772 46.328853 232.504759 35.531975 0.667212 0.552662 0.870669 0.510581 19.366126 2.368182 74.015548 144.484341
12 49.986412 4.351467 423.693965 67.399421 0.777049 0.372173 0.792595 0.615129 3.308259 13.283944 72.433127 167.542777
13 -139.930617 55.813951 31.197034 6.256484 0.862203 0.661667 0.627329 0.910606 0.957774 7.831456 159.225640 229.088549
14 36.764929 -252.956008 167.639525 21.050694 0.313875 0.141224 0.750266 0.509854 41.342928 10.301601 161.201313 101.877290
15 -210.002651 -29.660746 33.508269 80.902364 0.538023 0.570877 0.152049 0.501276 26.236782 25.037154 163.651548 83.332650
16 62.550802 24.132193 487.671567 14.692192 0.840108 0.185270 0.458324 0.050243 38.762203 28.064535 56.498054 2.756826
17 88.523148 -115.101408 408.486954 34.264515 0.989451 0.278643 0.351219 0.034912 11.721280 5.571992 124.390046 210.770524
18 -59.235596 38.632332 426.273711 86.465892 0.889519 0.218710 0.093777 0.551160 17.254187 11.175268 48.893973 204.250079
19 12.354770 -20.447122 468.982616 15.492531 0.371467 0.182838 0.486130 0.438179 1.505194 27.858917 34.309770 26.635902
20 195.415743 175.547570 42.551743 8.273684 0.195167 0.825711 0.920740 0.839180 48.074616 1.854254 33.233842 147.098632
21 -50.574670 157.301973 192.798796 48.453800 0.489393 0.285708 0.040059 0.160680 33.393395 2.770816 61.579372 118.315333
22 -105.890759 -46.580557 35.517445 30.241951 0.741641 0.927124 0.291461 0.024972 46.660254 4.883730 77.392372 30.270819
23 148.166340 -15.083771 105.396551 56.340836 0.492569 0.969927 0.207541 0.449039 13.274820 17.856385 149.570851 250.044898
24 196.258719 -7.394757 114.682889 80.380489 0.483181 0.571260 0.238147 0.237479 30.573181 4.514168 21.580397 54.747451
25 0.369567 -45.165948 234.553606 13.714849 0.838230 0.143001 0.908435 0.049614 33.924998 29.042291 132.286653 17.144716
26 101.146304 19.502498 134.281084 58.069908 0.361404 0.374548 0.468069 0.724598 15.877485 13.401436 95.661885 151.686082
27 134.147592 -75.828207 50.489053 50.550876 0.859795 0.797732 0.466299 0.111593 42.405462 15.045539 51.830162 188.411003
28 -74.248423 -113.061533 83.745545 14.407879 0.406805 0.367391 0.760576 0.608320 47.358073 7.399758 88.707525 8.273079
29 -48.530584 62.271122 73.637782 62.399849 0.328233 0.087017 0.154492 0.281050 44.242756 14.128808 53.989573 167.972998
X_pca
 ndarray (30 × 5) float32 (5 cols)
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~7.6 KB

16. Very Long Field Names

Tests the dynamic field name column width calculation. The longest field name is 'this_is_an_extremely_long_column_name_that_should_test_the_max_width_setting' (77 chars). The name column width should expand to fit longer names but be capped by repr_html_max_field_width (default: 400px). Names exceeding the max width show an ellipsis (...) via CSS text-overflow; hover over truncated names to see the full name in a tooltip.
AnnData 20 obs × 10 vars
obs_names: 0, 1, 2, 3, 4, ..., 15, 16, 17, 18, 19
var_names: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
X ndarray (20 × 10) float32
obs (4 columns) ?
short
 float64 (20 unique)
this_is_a_moderately_long_column_name
 float64 (20 unique)
this_is_an_extremely_long_column_name_that_should_test_the_max_width_setting
 float64 (20 unique)
cell_type_annotation_from_automated_classifier_v2
 category (2) AB
var (empty) ?
No entries
uns (1 items) ?
preprocessing_parameters_for_normalization_and_scaling
 dict {method, scale}
obsm (1 items) ?
X_pca_computed_with_highly_variable_genes_batch_corrected
 ndarray (20 × 5) float32 (5 cols)
varm (empty) ?
No entries
layers (1 items) ?
raw_counts_before_any_preprocessing_steps
 ndarray (20 × 10) float32
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~3.8 KB

17. README Icon

When uns['README'] contains a string, a small ⓘ icon appears in the header. Click the icon to open a modal with the README content rendered as markdown. The modal supports: headers (h1-h4), bold/italic, code blocks, inline code, ordered lists (numbered), unordered lists (bulleted), links, tables, and blockquotes. Press Escape or click outside to close.
AnnData 50 obs × 20 vars ⓘ
obs_names: 0, 1, 2, 3, 4, ..., 45, 46, 47, 48, 49
var_names: 0, 1, 2, 3, 4, ..., 15, 16, 17, 18, 19
X ndarray (50 × 20) float32
obs (1 columns) ?
cluster
 category (5) ABCDE
var (empty) ?
No entries
uns (2 items) ?
cluster_colors
 colors (5)
README
 str "# Human Lung Adenocarcinoma - Patient LU-A047 Single-cell RNA sequencing of a *primary* lung adenoc..."
obsm (1 items) ?
X_pca
 ndarray (50 × 10) float32 (10 cols)
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~10.8 KB

18. README Icon in No-JS Mode

In no-JS mode, the README icon still appears but clicking it won't open a modal. Instead, **hover over the icon** to see the README content as a tooltip (browser's native title attribute). The tooltip shows the first 500 characters of the README.
AnnData 20 obs × 10 vars ⓘ
obs_names: 0, 1, 2, 3, 4, ..., 15, 16, 17, 18, 19
var_names: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
X ndarray (20 × 10) float32
obs (1 columns) ?
batch
 category (2) batch1batch2
var (empty) ?
No entries
uns (1 items) ?
README
 str "# Dataset Information This dataset contains processed single-cell data. ## Key Features - 20 cells..."
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~2.0 KB

19. MuData (Multimodal Data)

Demonstrates how MuData can reuse anndata's HTML repr machinery by simply registering a SectionFormatter for the .mod attribute. The mod section shows each modality as an expandable nested AnnData (click the arrow to expand). All standard sections (obs, var, obsm, varm, uns, etc.) work automatically. This example has 3 modalities: RNA (100×50), ATAC (100×30), and Protein (80×20).
MuData 100 obs × 100 vars MuData
obs_names: 0, 1, 2, 3, 4, ..., 95, 96, 97, 98, 99
var_names: 0, 1, 2, 3, 4, ..., 15, 16, 17, 18, 19
X None
mod (3 items) ?
rna
 AnnData (100 × 50)
AnnData 100 obs × 50 vars
X ndarray (100 × 50) float32
obs (2 columns) ?
cell_type
 category (3) B cellNK cellT cell
n_counts
 int64 (100 unique)
var (2 columns) ?
gene_name
 str (50 unique)
highly_variable
 bool (2 unique)
uns (1 items) ?
cell_type_colors
 colors (3)
obsm (2 items) ?
X_pca
 ndarray (100 × 10) float32 (10 cols)
X_umap
 ndarray (100 × 2) float32 (2 cols)
varm (empty) ?
No entries
layers (1 items) ?
raw
 ndarray (100 × 50) float32
obsp (empty) ?
No entries
varp (empty) ?
No entries
atac
 AnnData (100 × 30)
AnnData 100 obs × 30 vars
X ndarray (100 × 30) float32
obs (2 columns) ?
peak_count
 int64 (96 unique)
tss_enrichment
 float64 (100 unique)
var (2 columns) ?
peak_name
 str (30 unique)
chr
 str (!) (22 unique)
uns (empty) ?
No entries
obsm (1 items) ?
X_lsi
 ndarray (100 × 15) float32 (15 cols)
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
prot
 AnnData (80 × 20)
AnnData 80 obs × 20 vars
X ndarray (80 × 20) float32
obs (1 columns) ?
protein_count
 int64 (77 unique)
var (2 columns) ?
protein_name
 str (20 unique)
isotype_control
 bool (2 unique)
uns (empty) ?
No entries
obsm (empty) ?
No entries
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
obs (5 columns) ?
rna:cell_type
 category (3) B cellNK cellT cell
rna:n_counts
 int64 (100 unique)
atac:peak_count
 int64 (96 unique)
atac:tss_enrichment
 float64 (100 unique)
prot:protein_count
 float64 (77 unique)
var (6 columns) ?
rna:gene_name
 str (!) (50 unique)
rna:highly_variable
 boolean (2 unique)
atac:peak_name
 str (!) (30 unique)
atac:chr
 str (!) (22 unique)
prot:protein_name
 str (!) (20 unique)
prot:isotype_control
 boolean (2 unique)
uns (2 items) ?
experiment
 str "multiome_sample_001"
processing_date
 str "2024-03-15"
obsm (3 items) ?
rna
 ndarray (100 × 1) bool (1 cols)
atac
 ndarray (100 × 1) bool (1 cols)
prot
 ndarray (100 × 1) bool (1 cols)
varm (3 items) ?
rna
 ndarray (100 × 1) bool (1 cols)
atac
 ndarray (100 × 1) bool (1 cols)
prot
 ndarray (100 × 1) bool (1 cols)
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~16 B

20. Unified Accessor + Section (spatial_demo)

Demonstrates the unified accessor + section pattern. The @register_anndata_namespace decorator registers both the accessor (adata.spatial_demo) AND a section in the HTML repr. The accessor class defines _repr_section_(self, context) which returns a list of FormattedEntry objects. Optional class attributes: section_after (positioning), section_display_name, section_tooltip. This is the recommended pattern for external packages (SpatialData, MuData) to add both functionality and visualization.
AnnData 50 obs × 20 vars
obs_names: 0, 1, 2, 3, 4, ..., 45, 46, 47, 48, 49
var_names: 0, 1, 2, 3, 4, ..., 15, 16, 17, 18, 19
X ndarray (50 × 20) float32
obs (1 columns) ?
cluster
 category (3) ABC
var (empty) ?
No entries
uns (1 items) ?
_spatial_images
 dict {hires, lowres, segmentation}
obsm (1 items) ?
X_spatial
 ndarray (50 × 2) float32 (2 cols)
spatial (3 items)
hires
 Image (1000, 1000, 3)
lowres
 Image (200, 200, 3)
segmentation
 Image (1000, 1000)
varm (empty) ?
No entries
layers (empty) ?
No entries
obsp (empty) ?
No entries
varp (empty) ?
No entries
anndata v0.13.0.dev115+g6f5e2223e ~7.5 KB