Package index

Pipeline wrapper

Wrapper function to process multi-FOV dataset or per-FOV data

fastReseg_flag_all_errors(): fastReseg_flag_all_errors

fastReseg_full_pipeline(): fastReseg_full_pipeline

fastReseg_perFOV_full_process(): fastReseg_perFOV_full_process

Preprocessing

Functions to prepare input data and get baseline

runPreprocess(): runPreprocess

get_baselineCT(): get_baselineCT

choose_distance_cutoff(): choose_distance_cutoff

estimate_MeanProfile(): estimate_MeanProfile

scoreGenesInRef(): scoreGenesInRef

getCellType_maxScore(): getCellType_maxScore

getScoreCellType_gene(): getScoreCellType_gene

Example data

Example data to use with tutorial

example_CellGeneExpr: per cell gene expression matrix based on raw transcript data files generated by SMI

example_baselineCT: Percentile profile for single cell distribution of transcript number and average tLLR score from example dataset for spatial transcriptional profiling of tissue

example_clust: Cluster assignment for cells based on per cell gene expression profile and reference profiles in example data set

example_refProfiles: Data for cell type specific reference profiles

mini_transcriptDF: Transcript level data frame from Example dataset for spatial transcriptional profiling of tissue

ori_CellStatsDF: Cell level data frame from Example dataset for spatial transcriptional profiling of tissue

ori_RawExprs: Cell x Gene expression matrix from Example dataset for spatial transcriptional profiling of tissue

Modular functions of pipeline

Functions to perform individual tasks for each FOV

runPreprocess(): runPreprocess

runSegErrorEvaluation(): runSegErrorEvaluation

runTranscriptErrorDetection(): runTranscriptErrorDetection

runSegRefinement(): runSegRefinement

Flag poor fitted cells

Functions to detect cell segmentation errors

runSegErrorEvaluation(): runSegErrorEvaluation

score_cell_segmentation_error(): score_cell_segmentation_error

Flag poor fitted transcripts

Functions to identify wrongly segmented transcript groups

runTranscriptErrorDetection(): runTranscriptErrorDetection

flag_bad_transcripts(): flag_bad_transcripts

groupTranscripts_dbscan(): groupTranscripts_dbscan

groupTranscripts_Delaunay(): groupTranscripts_Delaunay

createSpatialDelaunayNW_from_spatLocs(): createSpatialDelaunayNW_from_spatLocs

flagTranscripts_LDA_hyperplane(): flagTranscripts_LDA_hyperplane

Functions to evaluate neighborhood of flagged transcript groups and perform refinement

runSegRefinement(): runSegRefinement

prepResegDF(): prepResegDF

get_neighborhood_content(): get_neighborhood_content

getNeighbors_transDF(): getNeighbors_transDF

decide_ReSegment_Operations(): decide_ReSegment_Operations

update_transDF_ResegActions(): update_transDF_ResegActions

transDF_to_perCell_data(): transDF_to_perCell_data

Visualization

Auxillary function to visualize spatial pattern of transcript-level information of multiple cells

plotSpatialScoreMultiCells(): plotSpatialScoreMultiCells

Ultilties

Auxillary function to set parallel processing and digesting input files

numCores(): Get number of cores for parallelized operations

checkTransFileInputsAndLoadFirst(): checkTransFileInputsAndLoadFirst

prepare_perFOV_transDF(): prepare_perFOV_transDF

myFun_fov_load(): myFun_fov_load

Miscellaneous

Supporting functions of various purposes

check_config_leiden(): check_config_leiden

check_config_spatialNW(): check_config_spatialNW

checkAndPrepInputs_perFOV(): checkAndPrepInputs_perFOV

checkTypeLengthValue(): checkTypeLengthValue

compartment_and_add_extra(): compartment_and_add_extra

initializeAllSegRes(): initializeAllSegRes

makeDummyOuts_perFOV(): makeDummyOuts_perFOV

myFun_3point_singleCell(): myFun_3point_singleCell

run_igraph_leiden(): run_igraph_leiden

igraph_delete_edges(): igraph_delete_edges