R/standardize_celltypes.R

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

standardize_celltypes <- function(celltype_vector,
                                  allow_subtypes = FALSE) {
    if (allow_subtypes) {
        Cell_group_dict <- c(
            "astrocytes" = "astrocytes",
            "microglia" = "microglia",
            "oligo" = "oligo",
            "neurons" = "neurons",
            "brain" = "brain",
            ExcitatoryNeurons = "neurons (+)",
            InhibitoryNeurons = "neurons (-)",
            NigralNeurons = "neurons (nigral)",
            Microglia = "microglia",
            Oligodendrocytes = "oligo",
            Astrocytes = "astrocytes",
            OPCs = "OPCs"
        )
    } else {
        Cell_group_dict <- c(
            "astrocytes" = "astrocytes",
            "microglia" = "microglia",
            "oligo" = "oligo",
            "OPCs" = "oligo",
            "neurons" = "neurons",
            "neurons (+)" = "neurons",
            "neurons (-)" = "neurons",
            "neurons (nigral)" = "neurons",
            "brain" = "brain",
            ExcitatoryNeurons = "neurons",
            InhibitoryNeurons = "neurons",
            NigralNeurons = "neurons",
            Microglia = "microglia",
            Oligodendrocytes = "oligo",
            Astrocytes = "astrocytes"
        )
    }
    celltypes <- Cell_group_dict[celltype_vector]
    return(celltypes)
}