group the flagged transcript within each cell based on spatial clustering using dbscan
Usage
groupTranscripts_dbscan(
chosen_transcripts = NULL,
distance_cutoff = "auto",
transcript_df,
cellID_coln = "CellId",
transID_coln = "transcript_id",
transSpatLocs_coln = c("x", "y", "z")
)Arguments
- chosen_transcripts
the transcript_id of chosen transcript
- distance_cutoff
maximum molecule-to-molecule distance within same transcript group (default = "auto")
- transcript_df
the data.frame with transcript_id, target/geneName, x, y and cell_id
- 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
data frame of connected transcripts among chosen_transcripts #'
cellID_coln, orignal cell_ID
transID_coln, connected transcripts among chosen_transcripts
transSpatLocs_coln, spatial coordinates of transcript
transcript_group, group of chosen_transcripts
Details
For query cell, group flagged transcripts only based on their molecular distance to each other. When distance cutoff = 'auto', use 20% average XY cell range as cutoff. In case of no more than 3 flagged transcripts per cell, determine the grouping based on distance cutoff directly. In case of more transcripts per cell, use dbscan to group transcripts with distance_cutoff as eps and minPts = 1.