Skip to content

allow underscores in cell names #86

@dimalvovs

Description

@dimalvovs

currently hd method fails if there are underscores in the cell names due to the regex specified in https://github.com/DeshpandeLab/SpaceMarkers/blob/ead294d01081609773f6c055ecdbadf1cfe0f772/R/utils.R#L390C9-L390C54

reproducible example

  lrpairs <- read.csv(file = sprintf("%s/lr_pairs.csv", "~/data/lr_scores_tesdata/"), row.names = 1)
  ligand_scores <- read.csv(file = sprintf("%s/ligand_scores.csv", "~/data/lr_scores_tesdata/"), row.names = 1)
  receptor_scores <- read.csv(file = sprintf("%s/receptor_scores.csv", "~/data/lr_scores_tesdata/"), row.names = 1)
  calculate_lr_scores(ligand_scores,receptor_scores,lr_pairs=lrpairs, method = "geometric_mean", weighted = TRUE)

receptor_scores.csv
ligand_scores.csv
lr_pairs.csv

since cell types may have underscores in them, it would be good to change to a more robust regex.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions