cellestial 0.1.0__tar.gz

cellestial-0.1.0/PKG-INFO

@@ -0,0 +1,37 @@
+Metadata-Version: 2.1
+Name: cellestial
+Version: 0.1.0
+Summary: 
+Author: Zaf4
+Author-email: zafermolbio@gmail.com
+Requires-Python: >=3.11,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: anndata (>=0.11.0,<0.12.0)
+Requires-Dist: cairosvg (>=2.7.1,<3.0.0)
+Requires-Dist: lets-plot (>=4.5.1,<5.0.0)
+Requires-Dist: polars (>=1.13.0,<2.0.0)
+Requires-Dist: pooch (>=1.8.2,<2.0.0)
+Requires-Dist: pyarrow (>=18.0.0,<19.0.0)
+Requires-Dist: pycairo (>=1.27.0,<2.0.0)
+Requires-Dist: scanpy[leiden] (>=1.10.4,<2.0.0)
+Description-Content-Type: text/markdown
+
+# APIS
+
+Apis (not APIs) comes from honey bees
+An Interactive Single-Cell Plotting Tool over a ggplot-like API.
+
+## Installation
+
+```bash
+pip install apis
+```
+
+## Usage
+
+```python
+import scplot as sp
+```
+

cellestial-0.1.0/README.md

@@ -0,0 +1,16 @@
+# APIS
+
+Apis (not APIs) comes from honey bees
+An Interactive Single-Cell Plotting Tool over a ggplot-like API.
+
+## Installation
+
+```bash
+pip install apis
+```
+
+## Usage
+
+```python
+import scplot as sp
+```

cellestial-0.1.0/cellestial/core/scatterplot.py

@@ -0,0 +1,120 @@
+from __future__ import annotations
+
+from typing import Literal
+# Core scverse libraries
+import polars as pl
+
+# Data retrieval
+import scanpy as sc
+from lets_plot import (
+    LetsPlot,
+    aes,
+    element_blank,
+    element_line,
+    element_text,
+    geom_blank,
+    geom_jitter,
+    geom_point,
+    geom_violin,
+    gggrid,
+    ggplot,
+    ggsize,
+    ggtb,
+    guide_colorbar,
+    guides,
+    labs,
+    layer_tooltips,
+    scale_color_continuous,
+    scale_color_gradient,
+    scale_color_hue,
+    scale_color_viridis,
+    theme,
+    theme_classic,
+)
+
+LetsPlot.setup_html()
+
+
+
+def scatter(
+    data,
+    key: str = "leiden",
+    *,
+    dimensions: Literal["umap", "pca", "tsne"] = "umap",
+    size=0.8,
+    interactive: bool = False,
+    color_low: str = "#ffffff",
+    color_high: str = "#377eb8",
+):
+    if not isinstance(data, sc.AnnData):
+        raise ValueError("data must be an AnnData object")
+    # get the coordinates of the cells in the dimension reduced space
+    frame = pl.from_numpy(
+        data.obsm[f"X_{dimensions}"], schema=[f"{dimensions}1", f"{dimensions}2"]
+    ).with_columns(pl.Series("ID", data.obs_names))
+
+    # deterministic names
+    if key in ["leiden", "louvain"]:  # if it is a clustering
+        frame = frame.with_columns(
+            pl.Series("ID", data.obs_names), pl.Series("Cluster", data.obs[key])
+        )
+        # cluster scatter
+        scttr = (
+            ggplot(data=frame)
+            + geom_point(
+                aes(x=f"{dimensions}2", y=f"{dimensions}1", color="Cluster"),
+                size=size,
+                tooltips=layer_tooltips(["ID", "Cluster"]),
+            )
+            + scale_color_hue()
+        )
+    else:  # if it is a gene
+        # adata.X is a matrix , axis0 is cells, axis1 is genes
+        # find the index of the gene
+        index = data.var_names.get_indexer(
+            data.var_names[data.var_names.str.startswith(key)]
+        )  # get the index of the gene
+        frame = frame.with_columns(
+            pl.Series("ID", data.obs_names),
+            pl.Series(key, data.X[:, index].flatten().astype("float64")),
+        )
+        scttr = (
+            ggplot(data=frame)
+            + geom_point(
+                aes(x=f"{dimensions}2", y=f"{dimensions}1", color=key),
+                size=size,
+                tooltips=layer_tooltips(["ID", key]),
+            )
+            + scale_color_continuous(low=color_low, high=color_high)
+            + theme_classic()
+        )
+
+    # add common layers
+    scttr += (
+        ggsize(700, 500)
+        + theme_classic()
+        + theme(
+            axis_text_x=element_blank(),
+            axis_text_y=element_blank(),
+            #   axis_ticks_y=element_blank(),
+            #   axis_ticks_x=element_blank(),
+            text=element_text(color="#1f1f1f", family="Arial", size=12, face="bold"),
+            title=element_text(color="#1f1f1f", family="Arial"),
+            axis_title_x=element_text(
+                color="#3f3f3f",
+                family="Arial",
+                size=16,
+            ),
+            axis_title_y=element_text(color="#3f3f3f", family="Arial", size=16),
+            legend_text=element_text(color="#1f1f1f", size=10, face="plain"),
+            axis_line=element_line(color="#3f3f3f", size=0.2),
+        )
+        + labs(
+            x=f"{dimensions}2".upper(), y=f"{dimensions}1".upper()
+        )  # UMAP1 and UMAP2 rather than umap1 and umap2 etc.,
+    )
+
+    if interactive:
+        return scttr + ggtb()
+    else:
+        return scttr

cellestial-0.1.0/cellestial/decorators/util.py

@@ -0,0 +1,17 @@
+from lets_plot import ggtb
+
+def interactive(func):
+    def wrapper(*args, **kwargs):
+
+        inter = kwargs.get("interactive")
+        if inter is True:
+            return func(*args, **kwargs) + ggtb()
+        elif inter is False:
+            return func(*args, **kwargs)
+        else:
+            msg = f"expected True or False for  'interactive' argument, but received {inter}"
+            raise ValueError(msg)
+        
+    return wrapper
+
+

cellestial-0.1.0/pyproject.toml

@@ -0,0 +1,25 @@
+[tool.poetry]
+name = "cellestial"
+version = "0.1.0"
+description = ""
+authors = ["Zaf4 <zafermolbio@gmail.com>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.11"
+anndata = "^0.11.0"
+cairosvg = "^2.7.1"
+lets-plot = "^4.5.1"
+polars = "^1.13.0"
+pooch = "^1.8.2"
+pyarrow = "^18.0.0"
+pycairo = "^1.27.0"
+scanpy = {extras = ["leiden"], version = "^1.10.4"}
+
+
+[tool.poetry.group.dev.dependencies]
+ipykernel = "^6.29.5"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"