Man pages for jayaraman-lab/neuprintrExtra
Extra functions to analyze neuprint EM datasets
| addContraSide | Functions to deal with crossing to the bad side of the brain |
| combineRois | Sum a set of ROIs in a connection table or neuronBag |
| connectivityCluster | Clustering neurons based on connectivity tables |
| connectivityMatrix | Builds a connectivity matrix from a connection object |
| cos_dist | Distance measurements |
| cxRetyping | Convenience function to do all the CX neurons renaming |
| filter.neuronBag | Filter a neuronBag based on its 'names' field |
| get_col_name | Small utility to generate "type.from" kind of names |
| getConnectionTable | Get connection table of inputs and add meta |
| getIntraBag | Convenience to filter a neuronBag to just connections between... |
| getMeta | A cached version of 'neuprint_get_meta' |
| getNeuronsInRoiTable | Get all instances of neurons of types with non zero pre/post... |
| getRoiInfo | Formats the results of a roiInfo query in a nice table with... |
| getROISummary | Build a per roi summary of innervation for neurons in a... |
| getRoiTree | A wrapper around 'neuprint_ROI_hierarchy' returning a cleaned... |
| get_type2typePath | Builds a data frame of pathways between 2 collections of... |
| getTypesInRoiTable | Returns a neuronBag object of all the neurons forming... |
| getTypesTable | Returns a table with all neurons belonging to types exactly... |
| getTypeToTypeTable | Generate a table of type to type connections, keeping only... |
| haneschPlot | Plot a hanesch type plot based on a summary of ROI... |
| is.connectivityCluster | Test if x is a connectivityCluster object |
| is.neuronBag | Test if x is a neuronBag |
| lateralize_types | Retype neurons in a table according to L/R |
| neuprintrExtra-package | neuprintrExtra: Extra functions to analyze neuprint EM... |
| neuron2polygon | Transforms a nat neuron object into a polygon that can be... |
| neuronBag | Create a neuronBag |
| pathDf2graphDf | Convert a type-to-type pathway dataframe to a graph dataframe |
| plotClusters | Plot a connectivityCluster object |
| plotConnectivity | Plot a connectivity matrix |
| processConnectionTable | Internal function, exposed only for fringe cases like... |
| redefineTypeByBodyId | Retype according to sets of bodyids |
| redefineTypeByName | Retype neurons according to a grep pattern to be run on names |
| redefine_types | Redefine types in a table/neuronBag |
| retype.na | Fill in the type and name field in case they are NAs |
| roiOutline | Get 2D outlines for a ROI |
| roisPalette | Create a consistent palette for ROIs for plotting |
| scale_color_CX_supertype | A color scale for Central complex supertypes |
| scale_fill_CX_supertype | A fill scale for Central complex supertypes |
| selectRoiSet | Select a set of ROIs from a ROI hierarchy as the one... |
| selectSupertypeSet | Select a set of Supertypes from a Supertypes table as the one... |
| setClusters | Add a cluster column to the tables of a connectivityCluster... |
| simplifyConnectionTable | Change from a bodyid/partner/prepost to a from/to format |
| supertype | Gets a supertype from a type name, with various levels of... |
| supertype2Palette | A color scale for Central complex supertypes |
| tableChain2path | Link an arbitrary number of connection tables into a pathway... |
| tables2path | Multiply 2 connection tables or a pathway table and a... |
| typesInROI | Extract types participating in a significant connection in a... |
| typesPalette | Create a consistent palette for supertypes for plotting |
