Add display option for multi-scroll filter selection by column with threshold indicators (#203)

* initial work towards feature scroll filters

* scroll bars for filters

* relative spacing for scroll plot

* scroll filter plot threshold indicators

* binning and such

* [pre-commit.ci lite] apply automatic fixes

* fine tuning and docs

* linting

* address coderabbit review suggestions

* ignore notebook file imports

* [pre-commit.ci lite] apply automatic fixes

* addressing copilot review suggestions

* tighter kde plotting for y-axis visuals

* [pre-commit.ci lite] apply automatic fixes

* address coderabbit comment

* [pre-commit.ci lite] apply automatic fixes

* address coderabbit comments

* updates from jennas review

Co-Authored-By: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>

---------

Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>

Author: 3 people

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     -   id: check-yaml
     -   id: detect-private-key
 -   repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "v2.18.1"
+    rev: "v2.19.0"
     hooks:
     -   id: pyproject-fmt
 -   repo: https://github.com/codespell-project/codespell
@@ -50,7 +50,7 @@ repos:
     hooks:
     -   id: actionlint
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.15.5"
+    rev: "v0.15.6"
     hooks:
     -   id: ruff-format
     -   id: ruff-check

README.md

@@ -30,6 +30,12 @@ For 3D notebook display behavior:
 - Disable automatic trame switching with `display_options={"auto_trame_for_3d": False}`.
 - Force trame layout regardless of auto-detection with `display_options={"view": "trame"}`.
 
+For row display in notebook/widget tables:
+
+- CytoDataFrame respects pandas display settings (`display.max_rows`, `display.min_rows`).
+- When the table is larger than `display.max_rows`, the widget table inserts a midpoint ellipsis row (`…`) to indicate omitted rows.
+- You can control truncation behavior by changing pandas display options before rendering.
+
 📓 ___Want to see CytoDataFrame in action?___ Check out our [example notebook](docs/src/examples/cytodataframe_at_a_glance.ipynb) for a quick tour of its key features.
 
 > ✨ CytoDataFrame development began within **[coSMicQC](https://github.com/cytomining/coSMicQC)** - a single-cell profile quality control package.

docs/src/examples/cytodataframe_at_a_glance.ipynb

@@ -45,6 +45,7 @@
     [
         "Metadata_ImageNumber",
         "Cells_Number_Object_Number",
+        "Nuclei_Texture_Variance_RNA_5_03_256",
         "Image_FileName_OrigAGP",
         "Image_FileName_OrigDNA",
         "Image_FileName_OrigRNA",
@@ -305,6 +306,28 @@
     ]
 ][:3]
 
+# %%time
+# view nuclear speckles data with images and overlaid outlines from masks
+# and also apply a filter to only show rows where the value for
+# "Nuclei_Texture_Variance_DAPI_3_03_256".
+CytoDataFrame(
+    data=f"{nuclear_speckles_path}/test_slide1_converted.parquet",
+    data_context_dir=f"{nuclear_speckles_path}/images/plate1",
+    data_mask_context_dir=f"{nuclear_speckles_path}/masks/plate1",
+    display_options={
+        "filter_columns": ["Nuclei_Texture_Variance_DAPI_3_03_256"],
+    },
+)[
+    [
+        "Metadata_ImageNumber",
+        "Nuclei_Number_Object_Number",
+        "Nuclei_Texture_Variance_DAPI_3_03_256",
+        "Image_FileName_A647",
+        "Image_FileName_DAPI",
+        "Image_FileName_GOLD",
+    ]
+]
+
 # %%time
 # view ALSF pediatric cancer atlas plate BR00143976 with images
 cdf = CytoDataFrame(
@@ -356,7 +379,6 @@
 cdf[["ImageNumber", "ObjectNumber", "FileName_Nuclei"]][:3]
 # +
 # %%time
-
 # read 3d images with segmentation masks and show the
 # segmentation masks are also 3D.
 cdf = CytoDataFrame(

docs/src/examples/cytodataframe_at_a_glance.py

@@ -110,6 +110,7 @@ lint.select = [
 ]
 # Ignore `E402` and `F401` (unused imports) in all `__init__.py` files
 lint.per-file-ignores."__init__.py" = [ "E402", "F401" ]
+lint.per-file-ignores."docs/src/examples/cytodataframe_at_a_glance.py" = [ "E402" ]
 lint.per-file-ignores."src/cytodataframe/*.py" = [ "ANN401", "PLC0415" ]
 lint.per-file-ignores."src/cytodataframe/image.py" = [ "PLR2004" ]
 # ignore typing rules for tests