Zero cells remaining from runSegErrorEvaluation

[YuanningEric]

Hi,

Thank you for the development of this awesome tool. We encountered a bug from the runSegErrorEvaluationfunction. Could you please kindly advise?

This step is good

prep_res <- runPreprocess(
counts = counts,
clust = clust,
refProfiles = NULL,
score_baseline = NULL,
lowerCutoff_transNum = NULL,
higherCutoff_transNum= NULL,
imputeFlag_missingCTs = FALSE,
ctrl_genes = NULL,
svmClass_score_cutoff = -2,
molecular_distance_cutoff = 2.7,
cellular_distance_cutoff = 20,
transcript_df = transcript_df,
transDF_fileInfo = NULL, # data.frame info for multiple perFOV transcript data.frame files
transID_coln = 'UMI_transID',
transGene_coln = "target",
cellID_coln = 'CellId',
spatLocs_colns = c('x','y','z'),
extracellular_cellID = 0 # cell ID for extracellular transcript
)

score_GeneMatrix <- prep_res[['score_GeneMatrix']]
score_baseline <- prep_res[['cutoffs_list']][['score_baseline']]
lowerCutoff_transNum <- prep_res[['cutoffs_list']][['lowerCutoff_transNum']]
higherCutoff_transNum <- prep_res[['cutoffs_list']][['higherCutoff_transNum']]

cellular_distance_cutoff <- prep_res[['cutoffs_list']][['cellular_distance_cutoff']]
molecular_distance_cutoff <- prep_res[['cutoffs_list']][['molecular_distance_cutoff']]

flagCell_lrtest_cutoff = 5
svmClass_score_cutoff = -2

Zero cells remaining

outs <- runSegErrorEvaluation(

• score_GeneMatrix= score_GeneMatrix,
• transcript_df = transcript_df,
• cellID_coln = 'UMI_cellID',
• transID_coln = 'UMI_transID',
• transGene_coln = 'target',
• spatLocs_colns = c('x','y','z'),
• flagModel_TransNum_cutoff = 50)
  Found 6182 common genes among transcript_df and score_GeneMatrix.
  Found 1924 cells and assigned cell type based on the provided refProfiles cluster profiles.
  Run linear regreassion in 3 Dimension.
  No single cell with transcript number above model_cutoff = 50, skip the evaluation.
  Warning message:
  In score_cell_segmentation_error(chosen_cells = names(celltype_cellVector), :
  Below model_cutoff = 50, skip 1924 cells with fewer transcripts. Move forward with remaining 0 cells.

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