API
Import Squidpy as:
import squidpy as sq
Graph
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Create a graph from spatial coordinates. |
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Compute neighborhood enrichment by permutation test. |
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Compute co-occurrence probability of clusters. |
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Compute centrality scores per cluster or cell type. |
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Compute interaction matrix for clusters. |
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Calculate various Ripley's statistics for point processes. |
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Perform the permutation test as described in [Efremova et al., 2020]. |
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Calculate Global Autocorrelation Statistic (Moran’s I or Geary's C). |
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Identify spatially variable genes with Sepal. |
Image
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Process an image by applying a transformation. |
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Segment an image. |
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Calculate image features for all observations in |
Plotting
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Plot spatial omics data with data overlayed on top. |
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Plot spatial omics data with segmentation masks on top. |
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Plot neighborhood enrichment. |
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Plot centrality scores. |
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Plot cluster interaction matrix. |
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Plot the result of a receptor-ligand permutation test. |
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Plot Ripley's statistics for each cluster. |
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Plot co-occurrence probability ratio for each cluster. |
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Create a temporary |
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Plot a variable using a smooth regression line with increasing distance to an anchor point. |
Reading
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Read 10x Genomics Visium formatted dataset. |
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Read Vizgen formatted dataset. |
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Read Nanostring formatted dataset. |
Tools
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Build a design matrix consisting of distance measurements to selected anchor point(s) for each observation. |