Tools Shortcut
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Preprocessing: pp
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 |
Tools: tl
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 |
Plotting: pl
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 |
Helper Functions: hl
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 |