# Deconvolution of Spatial Transcriptomics Data Based on Neural Networks

## Documentation for package ‘SpatialDDLS’ version 1.0.1

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

## Help Pages

B C D E F G I L M P S T Z

## -- B --

barErrorPlot | Generate bar error plots
barPlotCellTypes | Bar plot of deconvoluted cell type proportions
blandAltmanLehPlot | Generate Bland-Altman agreement plots between predicted and expected cell type proportions of test data

## -- C --

calculateEvalMetrics | Calculate evaluation metrics on test mixed transcriptional profiles
cell.names | Get and set 'cell.names' slot in a 'PropCellTypes' object
cell.names-method | Get and set 'cell.names' slot in a 'PropCellTypes' object
cell.names<- | Get and set 'cell.names' slot in a 'PropCellTypes' object
cell.names<--method | Get and set 'cell.names' slot in a 'PropCellTypes' object
cell.types | Get and set 'cell.types' slot in a 'DeconvDLModel' object
cell.types-method | Get and set 'cell.types' slot in a 'DeconvDLModel' object
cell.types<- | Get and set 'cell.types' slot in a 'DeconvDLModel' object
cell.types<--method | Get and set 'cell.types' slot in a 'DeconvDLModel' object
corrExpPredPlot | Generate correlation plots between predicted and expected cell type proportions of test data
createSpatialDDLSobject | Create a 'SpatialDDLS' object

## -- D --

deconv.spots | Get and set 'deconv.spots' slot in a 'SpatialDDLS' object
deconv.spots-method | Get and set 'deconv.spots' slot in a 'SpatialDDLS' object
deconv.spots<- | Get and set 'deconv.spots' slot in a 'SpatialDDLS' object
deconv.spots<--method | Get and set 'deconv.spots' slot in a 'SpatialDDLS' object
DeconvDLModel | The DeconvDLModel Class
DeconvDLModel-class | The DeconvDLModel Class
deconvSpatialDDLS | Deconvolute spatial transcriptomics data using trained model
distErrorPlot | Generate box or violin plots showing error distribution

## -- E --

estimateZinbwaveParams | Estimate parameters of the ZINB-WaVE model to simulate new single-cell RNA-Seq expression profiles

## -- F --

features | Get and set 'features' slot in a 'DeconvDLModel' object
features-method | Get and set 'features' slot in a 'DeconvDLModel' object
features<- | Get and set 'features' slot in a 'DeconvDLModel' object
features<--method | Get and set 'features' slot in a 'DeconvDLModel' object

## -- G --

genMixedCellProp | Generate training and test cell type composition matrices
getProbMatrix | Getter function for the cell composition matrix

## -- I --

installTFpython | Install Python dependencies for SpatialDDLS
interGradientsDL | Calculate gradients of predicted cell types/loss function with respect to input features for interpreting trained deconvolution models

## -- L --

loadSTProfiles | Loads spatial transcriptomics data into a SpatialDDLS object
loadTrainedModelFromH5 | Load from an HDF5 file a trained deep neural network model into a 'SpatialDDLS' object

## -- M --

method | Get and set 'method' slot in a 'PropCellTypes' object
method-method | Get and set 'method' slot in a 'PropCellTypes' object
method<- | Get and set 'method' slot in a 'PropCellTypes' object
method<--method | Get and set 'method' slot in a 'PropCellTypes' object
mixed.profiles | Get and set 'mixed.profiles' slot in a 'SpatialDDLS' object
mixed.profiles-method | Get and set 'mixed.profiles' slot in a 'SpatialDDLS' object
mixed.profiles<- | Get and set 'mixed.profiles' slot in a 'SpatialDDLS' object
mixed.profiles<--method | Get and set 'mixed.profiles' slot in a 'SpatialDDLS' object
model | Get and set 'model' slot in a 'DeconvDLModel' object
model-method | Get and set 'model' slot in a 'DeconvDLModel' object
model<- | Get and set 'model' slot in a 'DeconvDLModel' object
model<--method | Get and set 'model' slot in a 'DeconvDLModel' object

## -- P --

plotDistances | Plot distances between intrinsic and extrinsic profiles
plotHeatmapGradsAgg | Plot a heatmap of gradients of classes / loss function wtih respect to the input
plots | Get and set 'plots' slot in a 'PropCellTypes' object
plots-method | Get and set 'plots' slot in a 'PropCellTypes' object
plots<- | Get and set 'plots' slot in a 'PropCellTypes' object
plots<--method | Get and set 'plots' slot in a 'PropCellTypes' object
plotSpatialClustering | Plot results of clustering based on predicted cell proportions
plotSpatialGeneExpr | Plot normalized gene expression data (logCPM) in spatial coordinates
plotSpatialProp | Plot predicted proportions for a specific cell type using spatial coordinates of spots
plotSpatialPropAll | Plot predicted proportions for all cell types using spatial coordinates of spots
plotTrainingHistory | Plot training history of a trained SpatialDDLS deep neural network model
preparingToSave | Prepare 'SpatialDDLS' object to be saved as an RDA file
prob.cell.types | Get and set 'prob.cell.types' slot in a 'SpatialDDLS' object
prob.cell.types-method | Get and set 'prob.cell.types' slot in a 'SpatialDDLS' object
prob.cell.types<- | Get and set 'prob.cell.types' slot in a 'SpatialDDLS' object
prob.cell.types<--method | Get and set 'prob.cell.types' slot in a 'SpatialDDLS' object
prob.matrix | Get and set 'prob.matrix' slot in a 'PropCellTypes' object
prob.matrix-method | Get and set 'prob.matrix' slot in a 'PropCellTypes' object
prob.matrix<- | Get and set 'prob.matrix' slot in a 'PropCellTypes' object
prob.matrix<--method | Get and set 'prob.matrix' slot in a 'PropCellTypes' object
project | Get and set 'project' slot in a 'SpatialDDLS' object
project-method | Get and set 'project' slot in a 'SpatialDDLS' object
project<- | Get and set 'project' slot in a 'SpatialDDLS' object
project<--method | Get and set 'project' slot in a 'SpatialDDLS' object
PropCellTypes | The PropCellTypes Class
PropCellTypes-class | The PropCellTypes Class

## -- S --

saveRDS | Save 'SpatialDDLS' objects as RDS files
saveRDS-method | Save 'SpatialDDLS' objects as RDS files
saveTrainedModelAsH5 | Save a trained 'SpatialDDLS' deep neural network model to disk as an HDF5 file
set | Get and set 'set' slot in a 'PropCellTypes' object
set-method | Get and set 'set' slot in a 'PropCellTypes' object
set.list | Get and set 'set.list' slot in a 'PropCellTypes' object
set.list-method | Get and set 'set.list' slot in a 'PropCellTypes' object
set.list<- | Get and set 'set.list' slot in a 'PropCellTypes' object
set.list<--method | Get and set 'set.list' slot in a 'PropCellTypes' object
set<- | Get and set 'set' slot in a 'PropCellTypes' object
set<--method | Get and set 'set' slot in a 'PropCellTypes' object
showProbPlot | Show distribution plots of the cell proportions generated by 'genMixedCellProp'
simMixedProfiles | Simulate training and test mixed spot profiles
simSCProfiles | Simulate new single-cell RNA-Seq expression profiles using the ZINB-WaVE model parameters
single.cell.real | Get and set 'single.cell.real' slot in a 'SpatialDDLS' object
single.cell.real-method | Get and set 'single.cell.real' slot in a 'SpatialDDLS' object
single.cell.real<- | Get and set 'single.cell.real' slot in a 'SpatialDDLS' object
single.cell.real<--method | Get and set 'single.cell.real' slot in a 'SpatialDDLS' object
single.cell.simul | Get and set 'single.cell.simul' slot in a 'SpatialDDLS' object
single.cell.simul-method | Get and set 'single.cell.simul' slot in a 'SpatialDDLS' object
single.cell.simul<- | Get and set 'single.cell.simul' slot in a 'SpatialDDLS' object
single.cell.simul<--method | Get and set 'single.cell.simul' slot in a 'SpatialDDLS' object
spatial.experiments | Get and set 'spatial.experiments' slot in a 'SpatialDDLS' object
spatial.experiments-method | Get and set 'spatial.experiments' slot in a 'SpatialDDLS' object
spatial.experiments<- | Get and set 'spatial.experiments' slot in a 'SpatialDDLS' object
spatial.experiments<--method | Get and set 'spatial.experiments' slot in a 'SpatialDDLS' object
SpatialDDLS | The SpatialDDLS Class
SpatialDDLS-class | The SpatialDDLS Class
SpatialDDLS-Rpackage | SpatialDDLS: an R package to deconvolute spatial transcriptomics data using deep neural networks
spatialPropClustering | Cluster spatial data based on predicted cell proportions

## -- T --

test.deconv.metrics | Get and set 'test.deconv.metrics' slot in a 'DeconvDLModel' object
test.deconv.metrics-method | Get and set 'test.deconv.metrics' slot in a 'DeconvDLModel' object
test.deconv.metrics<- | Get and set 'test.deconv.metrics' slot in a 'DeconvDLModel' object
test.deconv.metrics<--method | Get and set 'test.deconv.metrics' slot in a 'DeconvDLModel' object
test.metrics | Get and set 'test.metrics' slot in a 'DeconvDLModel' object
test.metrics-method | Get and set 'test.metrics' slot in a 'DeconvDLModel' object
test.metrics<- | Get and set 'test.metrics' slot in a 'DeconvDLModel' object
test.metrics<--method | Get and set 'test.metrics' slot in a 'DeconvDLModel' object
test.pred | Get and set 'test.pred' slot in a 'DeconvDLModel' object
test.pred-method | Get and set 'test.pred' slot in a 'DeconvDLModel' object
test.pred<- | Get and set 'test.pred' slot in a 'DeconvDLModel' object
test.pred<--method | Get and set 'test.pred' slot in a 'DeconvDLModel' object
topGradientsCellType | Get top genes with largest/smallest gradients per cell type
trainDeconvModel | Train deconvolution model for spatial transcriptomics data
trained.model | Get and set 'trained.model' slot in a 'SpatialDDLS' object
trained.model-method | Get and set 'trained.model' slot in a 'SpatialDDLS' object
trained.model<- | Get and set 'trained.model' slot in a 'SpatialDDLS' object
trained.model<--method | Get and set 'trained.model' slot in a 'SpatialDDLS' object
training.history | Get and set 'training.history' slot in a 'DeconvDLModel' object
training.history-method | Get and set 'training.history' slot in a 'DeconvDLModel' object
training.history<- | Get and set 'training.history' slot in a 'DeconvDLModel' object
training.history<--method | Get and set 'training.history' slot in a 'DeconvDLModel' object

## -- Z --

zinb.params | Get and set 'zinb.params' slot in a 'SpatialDDLS' object
zinb.params-method | Get and set 'zinb.params' slot in a 'SpatialDDLS' object
zinb.params<- | Get and set 'zinb.params' slot in a 'SpatialDDLS' object
zinb.params<--method | Get and set 'zinb.params' slot in a 'SpatialDDLS' object
ZinbParametersModel | The Class ZinbParametersModel
ZinbParametersModel-class | The Class ZinbParametersModel
zinbwave.model | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object
zinbwave.model-method | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object
zinbwave.model<- | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object
zinbwave.model<--method | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object