Man pages for SpatialDDLS
Deconvolution of Spatial Transcriptomics Data Based on Neural Networks
| barErrorPlot | Generate bar error plots |
| barPlotCellTypes | Bar plot of deconvoluted cell type proportions |
| blandAltmanLehPlot | Generate Bland-Altman agreement plots between predicted and... |
| calculateEvalMetrics | Calculate evaluation metrics on test mixed transcriptional... |
| cell.names | Get and set 'cell.names' slot in a 'PropCellTypes' object |
| cell.types | Get and set 'cell.types' slot in a 'DeconvDLModel' object |
| corrExpPredPlot | Generate correlation plots between predicted and expected... |
| createSpatialDDLSobject | Create a 'SpatialDDLS' object |
| DeconvDLModel-class | The DeconvDLModel Class |
| deconvSpatialDDLS | Deconvolute spatial transcriptomics data using trained model |
| deconv.spots | Get and set 'deconv.spots' slot in a 'SpatialExperiment'... |
| distErrorPlot | Generate box or violin plots showing error distribution |
| estimateZinbwaveParams | Estimate parameters of the ZINB-WaVE model to simulate new... |
| features | Get and set 'features' slot in a 'DeconvDLModel' object |
| genMixedCellProp | Generate training and test cell type composition matrices |
| getProbMatrix | Getter function for the cell composition matrix |
| installTFpython | Install Python dependencies for SpatialDDLS |
| interGradientsDL | Calculate gradients of predicted cell types/loss function... |
| loadSTProfiles | Loads spatial transcriptomics data into a SpatialDDLS object |
| loadTrainedModelFromH5 | Load from an HDF5 file a trained deep neural network model... |
| method | Get and set 'method' slot in a 'PropCellTypes' object |
| mixed.profiles | Get and set 'mixed.profiles' slot in a 'SpatialExperiment'... |
| model | Get and set 'model' slot in a 'DeconvDLModel' object |
| plotDistances | Plot distances between intrinsic and extrinsic profiles |
| plotHeatmapGradsAgg | Plot a heatmap of gradients of classes / loss function wtih... |
| plots | Get and set 'plots' slot in a 'PropCellTypes' object |
| plotSpatialClustering | Plot results of clustering based on predicted cell... |
| plotSpatialGeneExpr | Plot normalized gene expression data (logCPM) in spatial... |
| plotSpatialProp | Plot predicted proportions for a specific cell type using... |
| plotSpatialPropAll | Plot predicted proportions for all cell types using spatial... |
| plotTrainingHistory | Plot training history of a trained SpatialDDLS deep neural... |
| preparingToSave | Prepare 'SpatialDDLS' object to be saved as an RDA file |
| prob.cell.types | Get and set 'prob.cell.types' slot in a 'SpatialExperiment'... |
| prob.matrix | Get and set 'prob.matrix' slot in a 'PropCellTypes' object |
| project | Get and set 'project' slot in a 'SpatialExperiment' object |
| PropCellTypes-class | The PropCellTypes Class |
| saveRDS | Save 'SpatialExperiment' objects as RDS files |
| saveTrainedModelAsH5 | Save a trained 'SpatialDDLS' deep neural network model to... |
| set | Get and set 'set' slot in a 'PropCellTypes' object |
| set.list | Get and set 'set.list' slot in a 'PropCellTypes' object |
| showProbPlot | Show distribution plots of the cell proportions generated by... |
| simMixedProfiles | Simulate training and test mixed spot profiles |
| simSCProfiles | Simulate new single-cell RNA-Seq expression profiles using... |
| single.cell.real | Get and set 'single.cell.real' slot in a 'SpatialExperiment'... |
| single.cell.simul | Get and set 'single.cell.simul' slot in a 'SpatialExperiment'... |
| SpatialDDLS-class | The SpatialDDLS Class |
| SpatialDDLS-package | SpatialDDLS: Deconvolution of Spatial Transcriptomics Data... |
| SpatialDDLS-Rpackage | SpatialDDLS: an R package to deconvolute spatial... |
| spatial.experiments | Get and set 'spatial.experiments' slot in a... |
| spatialPropClustering | Cluster spatial data based on predicted cell proportions |
| test.deconv.metrics | Get and set 'test.deconv.metrics' slot in a 'DeconvDLModel'... |
| test.metrics | Get and set 'test.metrics' slot in a 'DeconvDLModel' object |
| test.pred | 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 'SpatialExperiment'... |
| training.history | Get and set 'training.history' slot in a 'DeconvDLModel'... |
| ZinbParametersModel-class | The Class ZinbParametersModel |
| zinb.params | Get and set 'zinb.params' slot in a 'SpatialExperiment'... |
| zinbwave.model | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel'... |
