mr-milk / spatialtis

Spatial analysis toolkit for single cell multiplexed tissue data

SpatialTis

SpatialTis is an ultra-fast spatial analysis toolkit for large-scale spatial single-cell data.

• ✔️ Spatial Transcriptome (Non single-cell)
• ✔️ Spatial Proteome (Single-cell)
• 🦀 Core algorithms implements in Rust
• 🚀 Parallel processing support

🔋 Highlighted spatial analysis

• Cell neighbors search (KD-Tree/R-Tree/Delaunay)
• Cell-Cell Interaction
• Marker spatial co-expression
• Spatial variable genes (current support: SOMDE)
• GCNG: Inferring ligand-receptor using graph convolution network
• Identify neighbor dependent markers

📦 Other analysis

• Spatial distribution
• Hotspot detection
• Spatial auto-correlation
• Spatial heterogeneity

Quick Start

Installation

pypi

SpatialTis requires Python >= 3.8.

pip install spatialtis

# For full features
pip install 'spatialtis[all]'

Install the current development version

pip install git+https://github.com/Mr-Milk/SpatialTis.git

Docker

docker pull mrmilk/spatialtis

To start a docker container:

cd your/data/
docker run -it --rm -p 8888:8888 -v "${PWD}:/analysis" spatialtis

• -it: Run the container in interactive mode
• -rm: Clean file system in container after shutting down
• If local port 8888 is taken, try -p 9999:8888 and change to 9999.
• -v: Mount your data directory to the working directory /analysis in the container. ${PWD} is the directory where you run this command. All changes made in this directory will be saved.

Low level API

If you are interested in using low level algorithms yourself, Please refer to spatialtis_core It provides clear document for all exposed API.

spatialtis's Issues

errors

Hi, this looks like a really useful package, I hope you are able to continue developing it!
I noted there were some bugs between the pip install spatialtis and pip install 'spatialtis[all]' with the capitilisation of Config/CONFIG between the two when calling this function throughout.
This issue is resolved in the latest github repository and I have been exploring the spatial .st.xxx function in the imc_data.h5ad dataset in your tutorial notebooks, however I see get some errors running the .sp.xxx code from your notebooks, which I have edited in line with the API readthedocs.
shown here for
sp.cell_components and sp.cell_co_occurrence.

these throw the same errors with my dataset - have there been changes to the sp. functions?

st.Config

sp.cell_components(data, groupby=['stage', 'part'], key='cell_components')

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[55], line 2
      1 islets_cells = ['gamma', 'delta', 'alpha', 'beta']
----> 2 sp.cell_components(data, groupby=['stage', 'part'])

File ~/miniconda3/envs/spatialtis/lib/python3.9/site-packages/spatialtis/plotting/basic.py:42, in cell_components(data, groupby, key, orient, type_order, **plot_options)
     39 data = data.groupby(groupby).sum().melt(
     40     ignore_index=False, value_name="Count").reset_index()
     41 data = data.rename(columns={'cell type': 'Cell Type'})
---> 42 return stacked_bar(data,
     43                    group=groupby,
     44                    value="Count",
     45                    stacked="Cell Type",
     46                    orient=orient,
     47                    **plot_options)

File ~/miniconda3/envs/spatialtis/lib/python3.9/site-packages/milkviz/_stacked_bar.py:88, in stacked_bar(data, group, value, stacked, orient, group_order, stacked_order, percentage, barwidth, cmap, colors, show_values, props, legend_kw, ax)
     86     stacked_order = natsorted(data[stacked].unique())
     87 if group_order is None:
---> 88     group_order = natsorted(data[group].unique())
     90 _, legend_labels, legend_colors = \
     91     cat_colors(stacked_order, stacked_order, cmap, colors)
     93 start_x = 1

File ~/miniconda3/envs/spatialtis/lib/python3.9/site-packages/pandas/core/generic.py:5902, in NDFrame.__getattr__(self, name)
   5895 if (
   5896     name not in self._internal_names_set
   5897     and name not in self._metadata
   5898     and name not in self._accessors
   5899     and self._info_axis._can_hold_identifiers_and_holds_name(name)
   5900 ):
   5901     return self[name]
-> 5902 return object.__getattribute__(self, name)

AttributeError: 'DataFrame' object has no attribute 'unique



sp.cell_co_occurrence(data, ['stage'], use="heatmap")
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[48], line 1
----> 1 sp.cell_co_occurrence(data, ['stage'], use="heatmap")

TypeError: cell_co_occurrence() got multiple values for argument 'use'```

IO for Spatial Coordination

Current we support reading from key in obs with wkt format.

Plan to support

• Key or keys in .obs, if it's a key with 'centroid' or 'spatial', it will be automatically interpreting as spatial coordinations. Can be either python sequence or Wkt string that fit in GeoPandas. If keys, two or three columns must be specified.
• Key in .obsm as 2D numpy array

Version 0.6.0

Hi,

Where is the v0.6.0 version of this software? Thank you!

Best,
Yang

`sp.cell_map` inconsistent cell type color between ROI

Allow customized colormap for sp.cell_map or store the color mapper in the anndata to allow consistent cell type color

Preprocessing to handle cell shape and centroid

The cell shape and centroid are stored as Python object in data frame, which cannot be stored on disk, may need to find another way to store it.

EXP_OBS failed when type are not str

When the dtype is not str from only one key in EXP_OBS, the processing will fail

`sp.cell_components` incorrect number on the plot

Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

Open

These updates have all been created already. Click a checkbox below to force a retry/rebase of any.

• Update codecov/codecov-action action to v3.1.6
• Update python Docker tag to v3.12
• Update actions/checkout action to v4
• Update actions/setup-python action to v5
• Update codecov/codecov-action action to v4
• Update dependency setuptools to v71
• Update docker/build-push-action action to v6
• Update docker/login-action action to v3
• Update docker/metadata-action action to v5
• Click on this checkbox to rebase all open PRs at once

Detected dependencies

dockerfile

Dockerfile

• python 3.10

benchmark/time-giotto.Dockerfile

benchmark/time-spatialtis.Dockerfile

• python 3

benchmark/time-squidpy.Dockerfile

• python 3.9

github-actions

.github/workflows/build.yml

• actions/checkout v3
• actions/setup-python v4
• docker/metadata-action v4
• docker/login-action v2
• docker/build-push-action v3

.github/workflows/docker-image.yaml

• actions/checkout v3
• docker/metadata-action v4
• docker/login-action v2
• docker/build-push-action v3

.github/workflows/test.yml

• actions/checkout v3
• actions/setup-python v4
• codecov/codecov-action v3.0.0
• actions/checkout v3
• actions/setup-python v4

pep621

pyproject.toml

• setuptools ~= 58.0
• setuptools_scm >=6.2

pip_requirements

requirements.ci.txt

requirements.txt

setup-cfg

setup.cfg

• spatialtis_core >= 0.2.3
• milkviz >= 0.6.0
• legendkit >= 0.2.5

---

• Check this box to trigger a request for Renovate to run again on this repository

Better handle of centroid and neighbors information in AnnData

Currently, we store the centroid and neighbors in the obs field, which will be parsed as string when read from disk, we need to eval them every time.

Centroid can be possible to store inobsm, since I may have a plan to fully support 3D in the future.

Neighbors' data is might need to move to uns, but we need to give each cell a UUID to track the neighbors.

Support visium data

Plan to support non-spatial single-cell data, it's more widely used.

spatial co-expression might use too many resource in transcriptome data

I May need to implement this in Rust or Cython, I prefer rust though.