Maps a character vector of column names to predefined cell type categories by matching against patterns, with optional regex support.
Usage
map_cell_groups(
column_names,
mapping_rules,
default_group = "Unknown",
verbose = FALSE,
use_regex = TRUE
)Arguments
- column_names
A character vector of column names to be mapped to cell type groups.
- mapping_rules
A named list where names are the target cell type groups and values are character vectors of patterns that identify columns belonging to each group.
- default_group
A string that represents the default group name for columns not matching any pattern. Default is "Unknown".
- verbose
Logical. If TRUE, prints mapping process messages showing which columns were mapped to which groups and which columns remained unmapped. Default is FALSE.
- use_regex
Logical. If TRUE (default), treats patterns in mapping_rules as regular expressions. If FALSE, performs exact string matching.
Value
A character vector with the same length as column_names,
containing the mapped cell type group for each column name. Columns that
don't match any pattern will be assigned the default_group.
Details
This function iterates through the mapping_rules list and
attempts to match each column name against the patterns for each cell type
group. The first matching group in the order of the list will be assigned.
When use_regex = TRUE, patterns are treated as regular expressions
and matching is case-insensitive. When use_regex = FALSE, exact
string matching is performed, which is case-sensitive.
Examples
# Example column names from a dataset
cols <- c("CD8_T_cell", "T_cell", "B_cell",
"NK_cell", "Monocyte", "Unknown_cell")
# Define simple mapping rules for cell types
mapping <- list(
"T_cell" = c("CD8_T_cell", "T_cell"),
"B_cell" = c("B_cell"),
"NK_cell" = c("NK_cell"),
"Monocyte" = c("Monocyte")
)
# Map column names to cell types using exact matching
cell_types <- map_cell_groups(cols, mapping, use_regex = FALSE)
print(data.frame(column = cols, cell_type = cell_types))
#> column cell_type
#> 1 CD8_T_cell T_cell
#> 2 T_cell T_cell
#> 3 B_cell B_cell
#> 4 NK_cell NK_cell
#> 5 Monocyte Monocyte
#> 6 Unknown_cell Unknown
# Define mapping rules using regex patterns
mapping_regex <- list(
"T_cell" = c("CD8.*", "T_cell"),
"B_cell" = c("B[-_]?cell"),
"NK_cell" = c("NK[-_]?cell"),
"Monocyte" = c("Mono.*")
)
# Map using regex patterns (default)
cell_types_regex <- map_cell_groups(cols, mapping_regex)
print(data.frame(column = cols, cell_type = cell_types_regex))
#> column cell_type
#> 1 CD8_T_cell T_cell
#> 2 T_cell T_cell
#> 3 B_cell B_cell
#> 4 NK_cell NK_cell
#> 5 Monocyte Monocyte
#> 6 Unknown_cell Unknown