Deconvolution of Spatial Transcriptomics Data Based on Neural
Networks
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘SpatialDDLS’ version 1.0.2
Help Pages
-- 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 |