# Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

## Documentation for package ‘CARDspa’ version 1.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

assign_sc_cords | The function to assign the spatial location information for each single cell
CARD-class | Each CARD object has a number of slots which store information. Key slots to access are listed below.
CARDfree | SpatialDeconv function based on Conditional Autoregressive model
CARDfree-class | Each CARDfree object has a number of slots which store information. Key slots to access are listed below.
CARDref | SpatialDeconv function based on Conditional Autoregressive model
CARD_deconvolution | Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics by CARD
CARD_imputation | Construct an enhanced spatial expression map on the unmeasured tissue locations
CARD_refFree | Extension of CARD into a reference-free version of deconvolution: CARDfree.
CARD_scmapping | Extension of CARD into performing single cell Mapping from non-single cell spatial transcriptomics dataset.
CARD_visualize_Cor | Visualize the cell type proportion correlation
CARD_visualize_gene | Visualize the spatial distribution of cell type proportion
CARD_visualize_pie | Visualize the spatial distribution of cell type proportion in a geom scatterpie plot
CARD_visualize_prop | Visualize the spatial distribution of cell type proportion
CARD_visualize_prop_2CT | Visualize the spatial distribution of two cell type proportions on the same plot
createCARDfreeObject | Create the CARD object
createCARDObject | Create the CARD object
create_ref | Construct the mean gene expression basis matrix (B), this is the faster version
get_high_res_cords | The function to sample the spatial location information for each single cell
get_weight_for_cell | The function to estimate the cell type composition signature for each single cell in the scRNaseq reference data
markerList | marker gene list
mvn_cv | Imputation and Construction of High-Resolution Spatial Maps for Cell Type Composition and Gene Expression by the spatial correlation structure between original spatial locations and new grided spatial locations
norm_coords_train_test | Normalize the new spatial locations without changing the shape and relative positions
sample_grid_within | Make new spatial locations on unmeasured tissue through grids.
sc_count | scRNA-seq count data
sc_meta | scRNAseq meta data
sc_QC | Quality control of scRNA-seq count data
select_info | Select Informative Genes used in the deconvolution
show-method | Show method for the CARD class
show-method | Show method for the CARDfree class
Sigma | Calculate the variance covariance matrix used in the imputation of the new grided locations
spatial_count | Spatial transcriptomics count data
spatial_location | Spatial location data