Man pages for CellTrails
Reconstruction, visualization and analysis of branching trajectories
| addTrail | ADD trail |
| connectStates | Connect trajectory states |
| contrastTrailExpr | Differential trail expression analysis |
| dot-adjustLayoutByPtime | Adjusting the trajectory graph layout |
| dot-bhtsne | #' DEF: Truncate eigenbasis #' #' For details see... |
| dot-capitalize | Capitalizes first character of string |
| dot-color_hue | Color palette |
| dot-color_ramp | Colors for vector |
| dot-connect_ordi | AUX Generate graph based on ordination |
| dot-connect_ortho | AUX: Connect orthogonal projected samples |
| dot-connectStates_def | DEF: Connect states |
| dot-contrastExprTrail_def | DEF: Differential expression between trails |
| dot-deleteMedianCentres | AUX Remove median centres |
| dot-denoiseExpression | Denoises expression |
| dot-diffExpr | Compute differential expression |
| dot-diffExprState_def | DEF: Differential expression between states |
| dot-embedSamples_def | DEF: Spectral embedding of samples |
| dot-exprs | GET expression matrix |
| dot-featureNameExists | Checks if feature exists |
| dot-filterTrajFeaturesByCOV_def | DEF: Filter features by coefficient of variation |
| dot-filterTrajFeaturesByDL_def | DEF: Filter feaures by Detection Level |
| dot-filterTrajFeaturesByFF_def | DEF: Filter features by index of dispersion / fano factor |
| dot-findSpectrum_def | DEF: Determine number of informative latent dimensions |
| dot-findStates_def | DEF: Find states |
| dot-fitDynamic_def | Fitting dynamics |
| dot-fit_surface | Fitting the map surface |
| dot-fitTrajectory_def | DEF: Trajectory fitting |
| dot-fr_layout | Computes state trajectory graph layout |
| dot-generate_ordination | AUX: Orthogonal projection ordination |
| dot-ihs | Reverse inverse hyperbolic sine |
| dot-linear_fit | Linear fit |
| dot-needsToBeExpanded | AUX Check if projection needs to be expanded |
| dot-nn_impute | Nearest neighbor imputation |
| dot-pca_def | DEF: PCA |
| dot-pheno | GET phenotype values |
| dot-phenoNameExists | Checks if phenotype exists |
| dot-plotDynamic | DEF: Visualize expression dynamic |
| dot-plotManifold_def | DEF: Visualizing the manifold |
| dot-plotSpectrum_def | DEF: Visualizing the spectrum definition |
| dot-plotStateExpression_def | DEF: Violine plots of genes |
| dot-plotStateSize_def | DEF: Visualizing states sizes |
| dot-plotStateTrajectory_def | DEF: Visualizing the trajectory graph |
| dot-plotTrailblazing_def | DEF: Visualizing trailblazing |
| dot-plotTrail_def | DEF: Visualize trail on map |
| dot-plot_trajectoryFit | DEF: Visualizing the trajectory fit |
| dot-prettyColorRamp | Pretty color ramp |
| dot-prettyString | Pretty string from array |
| dot-project_ortho | AUX: Orthogonal projection |
| dot-rbf | Radial basis function |
| dot-rescale | Rescale vector |
| dot-sampleNameExists | Checks if sample exists |
| dot-spanForest | GET state trajectory graph |
| dot-spanForest-set | SET state trajectory graph |
| dot-spatmed | Spatial median |
| dot-stateTrajLayout | GET state trajectory layout |
| dot-trailNameExists | Checks if trail exists |
| dot-trajGraph | GET trajectory graph |
| dot-trajGraph-set | SET trajectory graph |
| dot-trajLandmark | GET trajectory landmark annotation |
| dot-trajLandmark-set | SET trajectory landmark annotation |
| dot-trajResiduals-set | SET trajectory fitting residuals |
| dot-useFeature | GET trajectory features indicator |
| dot-useFeature-set | SET trajectory features indicator |
| dot-useSample | GET trajectory samples indicator |
| dot-useSample-set | SET trajectory samples indicator |
| dot-validatePlotParams | Validates parameter settings for plot methods |
| dot-write_ygraphml_def | DEF: Export trajectory graph |
| embedSamples | Spectral embedding of biological samples |
| enrichment.test | Enrichment test |
| exSCE | Example single-cell expression data |
| featureNames-SingleCellExperiment-method | GET feature names |
| filterTrajFeaturesByCOV | Filter features by Coefficient of Variation (COV) |
| filterTrajFeaturesByDL | Filter trajectory features by Detection Level (DL) |
| filterTrajFeaturesByFF | Filter features by Fano Factor |
| findSpectrum | Determine number of informative latent dimensions |
| findStates | Identify trajectory states |
| fitDynamic | Fit expression dynamic |
| fitTrajectory | Align samples to trajectory |
| landmarks | GET landmarks |
| latentSpace | GET CellTrails' latent space |
| latentSpace-set | SET latent space |
| manifold2D | GET 2D manifold representation |
| manifold2D-set | SET 2D manifold representation |
| pca | Principal Component Analysis |
| phenoNames | GET phenotype names |
| plotDynamic | Visualize dynamics |
| plotManifold | Visualize the learned manifold |
| plotMap | Visualize expression maps |
| plotStateExpression | Visualize feature expression distribution per state |
| plotStateSize | Visualize the number of samples per state |
| plotStateTrajectory | Visualize state trajectory graph |
| plotTrail | Visualize single trails |
| plotTrajectoryFit | Visualize trajectory fit residuals |
| read.ygraphml | Reads trajectory graph layout |
| removeTrail | REMOVE trail |
| sampleNames-SingleCellExperiment-method | GET sample names |
| selectTrajectory | Select component from trajectory graph |
| showTrajInfo | Shows relevant content of a SingleCellExperiment object for a... |
| simulate_exprs | Simulation of RNA-Seq expression data |
| states | GET states |
| states-set | SET states |
| stateTrajLayout-set | SET state trajectory layout |
| trailNames | GET trail names |
| trailNames-set | SET trail names |
| trails | GET trails |
| trajComponents | GET trajectory component states |
| trajFeatureNames | GET trajectory feature names |
| trajFeatureNames-set | SET trajectory features by name |
| trajLayout | GET trajectory layout |
| trajLayout-set | SET trajectory layout |
| trajResiduals | GET trajectory fitting residuals |
| trajSampleNames | GET trajectory sample names |
| userLandmarks | GET user-defined landmarks |
| userLandmarks-set | SET user-defined landmarks |
| write.ygraphml | Export trajectory graph |
