find neighbor cells of chosen_cells and return the relevant transcript data.frame for both query
Usage
getNeighbors_transDF(
chosen_cells = NULL,
neighbor_distance_xy = NULL,
transcript_df,
cellID_coln = "CellId",
transID_coln = "transcript_id",
transSpatLocs_coln = c("x", "y", "z")
)Arguments
- chosen_cells
the cell_ID of chosen cells need to be evaluate for re-segmentation
- neighbor_distance_xy
maximum cell-to-cell distance in x, y between the center of query cells to the center of neighbor cells with direct contact, same unit as input spatial coordinate. Default = NULL to use the 2 times of average cell diameter.
- transcript_df
the data.frame with transcript_id, cell_id and spatial coordinates
- cellID_coln
the column name of cell_ID in transcript_df
- transID_coln
the column name of transcript_ID in transcript_df
- transSpatLocs_coln
the column name of 1st, 2nd, optional 3rd spatial dimension of each transcript in transcript_df
Value
a data.frame
transcript_id, transcript id of all transcript near chosen cell's neighborhood
transSpatLocs_coln, coordinates
in_query_cell, flag whether current transcript is in the query cell, false means in neighbor cells
CellId, original cell id of each transcript
query_CellId, original query cell id of transcript's neighborhood
Details
get neighborhood transcript data frame for visualization
Locate neighbor cells of each query cell in 1st and 2nd dimension via cell-to-cell distance within neighbor_distance_xy. If no neighbor cells found for query cell, return query cell information only. Do not consider extracellular transcripts.