Man pages for pagoda2
Single Cell Analysis and Differential Expression
| areColors | Quick utility to check if given character vector is colors... |
| armaCor | armaCor - matrix column correlations. Allows faster matrix... |
| basicP2proc | Perform basic 'pagoda2' processing, i.e. adjust variance,... |
| basicP2web | Generate a 'pagoda2' web application from a 'Pagoda2' object |
| buildWijMatrix | Rescale the weights in an edge matrix to match a given... |
| calcMulticlassified | Returns a list vector with the number of cells that are... |
| cellsPerSelectionGroup | Get the number of cells in each selection group |
| cldend2array | Translate cell cluster dendrogram to an array, one row per... |
| collapse.aspect.clusters | Collapse aspect patterns into clusters |
| compareClusterings | Compare two different clusterings provided as factors by... |
| diffExprOnP2FromWebSelection | Perform differential expression on a p2 object given a set of... |
| diffExprOnP2FromWebSelectionOneGroup | Perform differential expression on a p2 object given a set of... |
| dot-onUnload | Correct unloading of the library |
| extendedP2proc | Perform extended 'Pagoda2' processing. Generate organism... |
| factorFromP2Selection | Returns a factor of cell membership from a p2 selection... |
| factorListToMetadata | Converts a list of factors into 'pagoda2' metadata optionally... |
| factorToP2selection | Converts a names factor to a p2 selection object if colors... |
| generateClassificationAnnotation | Given a cell clustering (partitioning) and a set of user... |
| gene.vs.molecule.cell.filter | Filter cells based on gene/molecule dependency |
| getCellsInSelections | Returns all the cells that are in the designated selections.... |
| getClusterLabelsFromSelection | Assign names to the clusters, given a clustering vector and a... |
| getColorsFromP2Selection | Retrieves the colors of each selection from a p2 selection... |
| get.control.geneset | Get a control geneset for cell scoring using the method... |
| get.de.geneset | Generate differential expression genesets for the web app... |
| getIntExtNamesP2Selection | Get a mapping form internal to external names for the... |
| hierDiffToGenesets | Converts the output of hierarchical differential expression... |
| make.p2.app | Generate a Rook Server app from a 'Pagoda2' object. This... |
| minMaxScale | Scale the designated values between the range of 0 and 1 |
| Mode | Return the mode of a vector |
| namedNames | Get a vector of the names of an object named by the names... |
| p2.generate.dr.go | Generate a GO environment for human for overdispersion... |
| p2.generate.dr.go.web | Generates zebrafish (Danio rerio) GO annotation for the web... |
| p2.generate.go | Generate a GO environment for the organism specified |
| p2.generate.go.web | Generates GO annotation for the web object for any species |
| p2.generate.go.web.fromGOEnv | Generates GO annotation for the web object from the GO... |
| p2.generate.human.go | Generate a GO environment for human for overdispersion... |
| p2.generate.human.go.web | Generates human GO annotation for the web object |
| p2.generate.mouse.go | Generate a GO environment for mouse for overdispersion... |
| p2.generate.mouse.go.web | Generates mouse (Mus musculus) GO annotation for the web... |
| p2.make.pagoda1.app | Create 'PAGODA1' web application from a 'Pagoda2' object... |
| p2.metadata.from.factor | Generate a list metadata structure that can be passed to a... |
| p2.toweb.hdea | Generate a 'pagoda2' web object from a 'Pagoda2' object using... |
| p2ViewPagodaApp | p2ViewPagodaApp R6 class |
| Pagoda2 | Pagoda2 R6 class |
| pagoda2WebApp | pagoda2WebApp class to create 'pagoda2' web applications via... |
| pagoda2WebApp_arrayToJSON | pagoda2WebApp_arrayToJSON |
| pagoda2WebApp_availableAspectsJSON | pagoda2WebApp_availableAspectsJSON |
| pagoda2WebApp_call | pagoda2WebApp_call |
| pagoda2WebApp_cellmetadataJSON | pagoda2WebApp_cellmetadataJSON |
| pagoda2WebApp_cellOrderJSON | pagoda2WebApp_cellOrderJSON |
| pagoda2WebApp_geneInformationJSON | pagoda2WebApp_geneInformationJSON |
| pagoda2WebApp_generateDendrogramOfGroups | Generate a dendrogram of groups |
| pagoda2WebApp_generateEmbeddingStructure | pagoda2WebApp_generateEmbeddingStructure |
| pagoda2WebApp_generateGeneKnnJSON | pagoda2WebApp_generateGeneKnnJSON |
| pagoda2WebApp_getCompressedEmbedding | pagoda2WebApp_getCompressedEmbedding |
| pagoda2WebApp_packCompressFloat64Array | pagoda2WebApp_packCompressFloat64Array |
| pagoda2WebApp_packCompressInt32Array | pagoda2WebApp_packCompressInt32Array |
| pagoda2WebApp_readStaticFile | pagoda2WebApp_readStaticFile |
| pagoda2WebApp_reducedDendrogramJSON | pagoda2WebApp_reducedDendrogramJSON |
| pagoda2WebApp_serializeToStaticFast | pagoda2WebApp_serializeToStaticFast |
| pagoda2WebApp_serverLog | pagoda2WebApp_serverLog |
| pagoda2WebApp_sparseMatList | pagoda2WebApp_sparseMatList |
| pagoda.reduce.loading.redundancy | Collapse aspects driven by the same combinations of genes.... |
| pagoda.reduce.redundancy | Collapse aspects driven by similar patterns (i.e. separate... |
| papply | Parallel, optionally verbose lapply. See ?parallel::mclapply... |
| pathway.pc.correlation.distance | Calculate correlation distance between PC magnitudes given a... |
| plotMulticlassified | Plot multiclassified cells per selection as a percent barplot |
| plotOneWithValues | Plot the embedding of a 'Pagoda2' object with the given... |
| plotSelectionOverlaps | Get a dataframe and plot summarising overlaps between... |
| projectKNNs | Project a distance matrix into a lower-dimensional space.... |
| read.10x.matrices | Quick loading of 10X CellRanger count matrices |
| read10xMatrix | This function reads a matrix generated by the 10x processing... |
| readPagoda2SelectionAsFactor | Read a pagoda2 cell selection file and return it as a factor... |
| readPagoda2SelectionFile | Reads a 'pagoda2' web app exported cell selection file... |
| removeSelectionOverlaps | Remove cells that are present in more than one selection from... |
| score.cells.nb0 | Score cells by getting mean expression of genes in signatures |
| score.cells.nb1 | Score cells after standardising the expression of each gene... |
| score.cells.puram | Puram, Bernstein (Cell, 2018) Score cells as described in... |
| sgdBatches | Calculate the default number of batches for a given number of... |
| show.app | Directly open the 'pagoda2' web application and view the... |
| sn | Set names equal to values, a stats::setNames wrapper function |
| subsetSignatureToData | Subset a gene signature to the genes in the given matrix with... |
| tp2c.view.pathways | View pathway or gene-weighted PCA 'Pagoda2' version of the... |
| validateSelectionsObject | Validates a pagoda2 selection object |
| view.aspects | Internal function to visualize aspects of transcriptional... |
| webP2proc | Generate a 'pagoda2' web object |
| winsorize.matrix | Sets the ncol(mat)*trim top outliers in each row to the next... |
| writeGenesAsPagoda2Selection | Writes a list of genes as a gene selection that can be loaded... |
| writePagoda2SelectionFile | Writes a pagoda2 selection object as a p2 selection file that... |
