Function reference • spacedeconv

Setup

set_cibersort_binary(): Set Path to CIBERSORT R script (CIBERSORT.R)

set_cibersort_mat(): Set Path to CIBERSORT matrix file (LM22.txt)

Datatype conversion

anndata_to_singlecellexperiment(): Convert AnnData to SingleCellExperiment

anndata_to_spatialexperiment(): Convert AnnData to SpatialExperiment

seurat_to_spatialexperiment(): Convert Seurat to SpatialExperiment

subsetSCE(): Subset Single Cell Experiment

subsetSPE(): Subset a SpatialExperiment Object

spe_to_ad(): Convert Spatial Experiment to AnnData

Main Workflow

deconvolution_methods: List of supported deconvolution methods

preprocess(): Preprocess SingleCellExperiments and Spatial Experiments

normalize(): Normalize Expression Object

build_model(): Build a reference signature

deconvolute(): Deconvolution with spacedeconv

build_and_deconvolute(): Build Model and Deconvolute in one step

available_results(): Check wich deconvolutionr results are available in a SpatialExperiment object

Custom access to methods

build_model_card(): No signature calculated, just call the deconvolute method

build_model_cell2location(): Build Model Cell2location

build_model_immunedeconv(): No signature calculated, just call the deconvolute method

build_model_omnideconv(): Build Reference

build_model_rctd(): RCTD builds the model internally, please just use the deconvolute method

build_model_spatial_dwls(): Build Model Spatial DWLS

build_model_spotlight(): Build Model SPOTlight

deconvolute_card(): Deconvolute CARD

deconvolute_cell2location(): Deconvolute Cell2location

deconvolute_immunedeconv(): Deconvolute Immundeconv

deconvolute_immunedeconv_mouse(): Deconvolute Immunedeconv mouse

deconvolute_omnideconv(): Deconvolute Omnideconv

deconvolute_rctd(): RCTD Deconvolution

deconvolute_spatial_dwls(): Deconvolute Spatial DWLS

deconvolute_spotlight(): Deconvolute SPOTlight

Visualization

plot_gene(): Function to plot gene expression

plot_celltype(): Function to plot deconvolution results

plot_umi_count(): Function to plot deconvolution results

plot_ndetected_genes(): Plot number of detected genes

plot_most_abundant(): Function to plot deconvolution results

plot_celltype_presence(): Plot celltype presence absence

plot_comparison(): Plot celltype fraction comparison

plot_scatter(): Benchmarking scatterplot to compare two spatial objects

plot_overview(): Plot Overview of a SpatialExperiment

Sample Data

single_cell_data_1: Example single cell dataset 1 from Wu et al.

single_cell_data_2: Example single cell dataset 2 from Wu et al.

single_cell_data_3: Example single cell dataset 3 from Wu et al.

single_cell_data_4: Example single cell dataset 4 from Wu et al.

spatial_data_1: Example spatial dataset 1 from Wu et al.

spatial_data_2: Example spatial dataset 2 from Wu et al.

spatial_data_3: Example spatial dataset 3 from Wu et al.

spatial_data_4: Example spatial dataset 4 from Wu et al.

Utils

aggregate_results(): Aggregate Deconvolution Results

annotate_spots(): Annotate spots

addCustomAnnotation(): Add Custom Annotation to a SpatialExperiment

cluster(): Cluster spacedeconv results

get_cluster_features(): Get cluster features

print_info(): Print info about dataset

filter_sample_id(): Filter SPE to contain only one sample ID

compare_signatures(): Compare Signatures

convert_human_to_mouse(): map human to mouse genes

convert_mouse_to_human(): map mouse to human genes

spatialcorr(): create a correlation plot

get_lr(): Compute L-R score for each spot

gene_set_score(): Calculate Gene Set Score

scale_cell_counts(): Scale relative cell fractions to absolute by providing cell densities

Metacell

clean_genes_and_cells(): Clean Genes and Cells with Metacell2

compute_forbidden_genes(): Compute forbidden genes

extract_forbidden_from_modules(): extract forbidden genes from gene modules

compute_metacells(): Compute Metacells

plot_metacell_nCells(): Plot the number of genes per metacells

plot_metacell_abundance(): Plot metacell abundance score

Colocalization

presence() presence(): Threshold a matrix

antimode_cutoff() antimode_cutoff(): Determine threshold for celltype presence based on antimode of celltype density

cell_pair_localization(): Cell pair colocalization or avoidance

cell_pair_presence(): Calculate Colocalization

coloc_avoid(): Colocalization of two celltypes

get_iniche(): Calculate Iniche recursivley

ripleys_k(): Ripley´s K celltype distribution

localization_heatmap(): Heatmaps cell pair localization and correlation of scores

qualitycontrol(): Quality control function

corr_expr(): Heatmap correlation of cell types based on gene expression values

plot_ripleys_k(): Combined Ripley´s K statistics in one plot

DecoupleR

get_decoupleR_reference(): Obtain a decoupleR reference

compute_activities(): Compute Pathway activities with decoupleR