Function reference • SpaCET

SpaCET object

SpaCET-class: Define the SpaCET object

create.SpaCET.object(): Create a SpaCET object

create.SpaCET.object.10X(): Create a SpaCET object from 10X Visium

SpaCET.quality.control(): Filter spatial spots and calculate the QC metrics

convert.Seurat(): Convert Seurat to SpaCET

addTo.Seurat(): Add SpaCET to Seurat

Deconvolution of ST data

SpaCET.deconvolution(): Deconvolve tumor ST data set

SpaCET.deconvolution.malignant(): Deconvolve malignant cell fraction

SpaCET.deconvolution.matched.scRNAseq(): Deconvolve ST data set with matched scRNAseq data

SpaCET.deconvolution.malignant.customized.scRNAseq(): Deconvolve malignant fraction with customized scRNAseq data

Cell-cell interaction analysis

SpaCET.CCI.colocalization(): Cell-cell colocalization analysis

SpaCET.CCI.LRNetworkScore(): Ligand-Receptor interaction enrichment analysis

SpaCET.CCI.cellTypePair(): Ligand-Receptor analysis for a co-localized cell-type pair

Tumor-Stroma Interface

SpaCET.identify.interface(): Identify tumor-stroma interface

SpaCET.combine.interface(): Combine interaction spots to interface

SpaCET.distance.to.interface(): Distance to tumor border

Visualization

SpaCET.visualize.spatialFeature(): Spatial feature visualization

SpaCET.visualize.colocalization(): Cell-cell colocalization visualization

SpaCET.visualize.cellTypePair(): Cell-type pair visualization

Gene set score calculation

SpaCET.GeneSetScore(): Calculate gene set score for each spot

read.gmt(): Read a gmt file

write.gmt(): Write a gmt file