Tools Shortcut

import scimap as sm

Scimap provides a suite of tools to preprocess the data for subsequent analysis.

Function	Short Description
`sm.pp.mcmicro_to_scimap`	`mcmicro` output to scimap compatible object
`sm.pp.rescale`	Manual/Auto gate based scaling of data
`sm.pp.combat`	Batch correction tool


`sm.tl.phenotype_cells`	Probability distribution based cell phenotyping
`sm.tl.cluster`	Cluster or sub-cluster single-cells using a variety of algorithms
`sm.tl.umap`	Dimensionality Reduction using UMAP
`sm.tl.foldchange`	Compute foldchange in phenotypes between samples/ROIs
`sm.tl.spatial_distance`	Computes nearest distance between all phenotypes for every cell
`sm.tl.spatial_interaction`	cell–cell interactions analysis
`sm.tl.spatial_count`	Distribution of cell-types with local neighborhood
`sm.tl.spatial_lda`	Latent Dirichlet Allocation (LDA) modelling for spatial motifs
`sm.tl.spatial_expression`	Distribution of spatial expression with local neighborhood
`sm.tl.spatial_cluster`	Distribution of spatial expression with local neighborhood
`sm.tl.spatial_pscore`	Scoring proximity between user defined cell types
`sm.tl.spatial_aggregate`	Aggregates of cell-types with local neighborhood
`sm.tl.spatial_similarity_search`	Search for similar looking regions within and across images


`sm.pl.image_viewer`	Opens the image with overlays on a `napari` browser
`sm.pl.addROI_image`	Add ROI's with `napari` browser
`sm.pl.gate_finder`	Overlays gating positivity on the image for manual gating
`sm.pl.distPlot`	Distribution plot of a given marker
`sm.pl.densityPlot2D`	2D density plotting of marker expression
`sm.pl.cluster_plots`	Meta function that outputs umap, heatmap and ranked makers for each group
`sm.pl.umap`	Overlays markers on UMAP
`sm.pl.foldchange`	vizualize foldchange in phenotypes between samples/ROIs
`sm.pl.spatial_scatterPlot`	Scatter plots of spatially resolved data
`sm.pl.spatial_distance`	Visualize distance between phenotypes
`sm.pl.spatial_interaction`	Heatmap of cell–cell interaction analysis
`sm.pl.spatial_pscore`	Bar plot of the derived Spatial Proximity Scores
`sm.pl.stacked_barplot`	Generate a stacked barplot from any two columns of categorical data
`sm.pl.pie`	Generate a pieplot of cell-type proportion or any categorical data
`sm.pl.voronoi`	Generate a voronoi diagram and color it with categorical data


`sm.hl.classify`	Quickly classify cells based on pos/negativity of list of markers
`sm.hl.rename`	Quickly rename values within columns based on `dict` mapping
`sm.hl.addROI_omero`	Add ROI's extracted from Omero to Scimap object
`sm.hl.dropFeatures`	Handy Function to subset the `adata` object
`sm.hl.animate`	Create a animated scatter plot of `embedding -> physical location`
`sm.hl.scimap_to_csv`	Export scimap object to CSV