API index

Everything scimappro exports, in one place. import scimappro as sp throughout.

import scimappro as sp

sp.pp — preprocessing

Function	What it does
mcmicro_to_scimap	Turn mcmicro-style quantification CSVs into an AnnData.
log1p	Chunked, parallel log1p of the expression matrix into a layer.
rescale	Rescale each marker to a 0–1 scale around its gate, fitting a GMM when no gate is given.
combat	ComBat batch correction across images or any other batch column.
nGraph	Build an igraph k-nearest-neighbour graph from the marker matrix.
dropFeatures	Drop markers, cells, obs columns, or whole phenotype groups.
mergeAdataObs	Merge obs from several objects covering the same cells.
scimapToCsv	Export expression plus obs to a flat CSV.
toSpatialData	Convert an AnnData into a scverse SpatialData store.

sp.tl — tools

Cell identity

Function	What it does
phenotype	Hierarchical, prior-knowledge cell typing from a gating workflow.
cluster	kmeans / leiden / dbscan over expression, or over a neighbourhood matrix with mode="spatial".
umap	UMAP embedding into obsm.
classify	Label cells by simple positive/negative marker rules.
rename	Collapse or relabel categories into a new obs column.
foldChange	Fold change in cell-type abundance between groups, with p-values.

Spatial statistics

Function	What it does
spatialDistance	Average distance between every pair of cell types.
spatialCooccurrence	Adjacency enrichment against a permutation null.
spatialProximityScore	Proximity volume and density for a chosen pair of cell types.
spatialAggregate	Find local aggregates of one cell type above a purity threshold.
spatialSimilarityLookup	Score every cell by similarity to a reference ROI's neighbourhood.

Cellular neighbourhoods

Function	What it does
neighCount	Per-cell counts of neighbouring cell types (or markers).
neighExp	Neighbourhood-weighted expression (spatial lag).
neighLDA	Latent Dirichlet Allocation motifs over neighbourhood composition.
neighNMF	Non-negative matrix factorisation motifs over neighbourhood composition.

sp.pl — plotting

Expression and composition

Function	What it does
heatmap	Mean marker expression per group, optionally clustered.
barplot	Stacked or grouped composition bars, matplotlib or plotly.
pie	Cell-type proportions as pie charts, faceted by group.
distPlot	Per-marker intensity distributions with gate lines.
densityPlot2D	Two-marker density, the biaxial gating view.
markerCorrelation	Marker–marker correlation heatmap.
groupCorrelation	Correlation of group composition across a condition.

Embeddings and clusters

Function	What it does
clusterPlots	UMAP, heatmap, and ranked markers for a set of clusters.
umap	Scatter of a UMAP embedding coloured by anything.
foldChange	Fold-change heatmap or parallel-coordinates plot.

Spatial

Function	What it does
spatialScatterPlot	Cells at their real coordinates, coloured by phenotype or marker.
voronoi	Voronoi tessellation coloured by cell type.
spatialDistance	Dispatcher for the two spatial-distance views.
spatialDistanceHeatmap	Cell-type × cell-type distance heatmap.
spatialDistanceDistribution	Distance distributions, faceted.
spatialCooccurrence	Co-occurrence heatmap with non-significant pairs greyed out.
spatialInteractionNetwork	Significant interactions as a node–edge network.
spatialProximityScore	Proximity volume/density bars.

Images and ROIs

Function	What it does
image_viewer	Overlay cells on the raw OME-TIFF in napari. Needs the qt extra.
addRoiScatter	Draw ROIs interactively on a scatter of cell positions.
addRoiImage	Draw ROIs on the raw image.

sp.helpers

Function	What it does
addROI_omero	Attach ROIs exported from OMERO to the cell table. Needs the roi extra.

Parameters every function shares

Parameter	Meaning
data	First argument, always. AnnData, .h5ad path, SpatialData, or .zarr store.
outputDir	Write the result here instead of returning it. None returns the object.
streamData	Run out of core against an .h5ad path. See Streaming.
sdataTable	Last named parameter, always. Which SpatialData table to use. See SpatialData.
maxWorkers	Cap on parallel workers. Defaults to max(1, cpu_count() - 1).
verbose	Progress messages.
label	Key under which results are written to obs, uns, layers, or obsm.

Plotting functions instead share show, returnData, returnFig, dpi, transparent, fileName, and outputDir.

saveDir is deprecated

A few plotting functions (heatmap, pie, foldChange, voronoi, the correlation and spatial-result plots) still accept saveDir alongside outputDir for scripts carried over from scimap. outputDir wins when both are given. Use outputDir.