R/utils.R

In hansenlab/tricycle: tricycle: Transferable Representation and Inference of cell cycle

.gg_theme <- theme_bw(base_size = 8) +
    theme(
        panel.grid.minor = element_blank(),
        panel.grid.major.x = element_blank(),
        panel.grid.major.y = element_line(size = 0.25),
        axis.ticks = element_line(colour = "black", linetype = 1, size = 0.25),
        axis.text.y = element_text(size = 6),
        axis.text.x = element_text(size = 6, vjust = 0.5, hjust = 0.5),
        axis.title.y = element_text(size = 7),
        axis.title.x = element_text(size = 7),
        plot.title = element_text(face = "plain", size = 8, hjust = 0.5),
        plot.margin = unit(c(5, 5, 6, 6), "pt"),
        legend.background = element_blank(),
        legend.position = "right",
        legend.justification = c(0.5, 0.5),
        legend.key.size = unit(7, "pt"),
        legend.key = element_blank(),
        legend.margin = margin(t = 1, r = 2, b = 2, l = 2, unit = "pt"),
        legend.title = element_text(size = 5),
        legend.title.align = 0.5,
        legend.text.align = 0.5,
        legend.text = element_text(size = 5),
        strip.text = element_text(color = "white"),
        strip.background = element_rect(fill = "black", color = "black")
    )


#' @importFrom methods is
#' @importClassesFrom AnnotationDbi AnnotationDb
.getAnnotationDB <- function(AnnotationDB = NULL, species = c("mouse", "human")) {
    species <- match.arg(species)
    if (!is.null(AnnotationDB)) {
        stopifnot("The input AnnotationDB is not an AnnotationDb object.", is(AnnotationDB, "AnnotationDb"))
    } else {
        if (species == "mouse") {
            stopifnot("No AnnotationDB input and org.Mm.eg.db package is not installed. Please install org.Mm.eg.db package." = nzchar(system.file(package = "org.Mm.eg.db")))
            AnnotationDb <- org.Mm.eg.db::org.Mm.eg.db
            message("No AnnotationDb desginated. org.Mm.eg.db will be used to map Mouse ENSEMBL id to gene SYMBOL.")
        } else {
            stopifnot("No AnnotationDB input and org.Hs.eg.db package is not installed. Please install org.Mm.Hs.db package." = nzchar(system.file(package = "org.Hs.eg.db")))
            AnnotationDb <- org.Hs.eg.db::org.Hs.eg.db
            message("No AnnotationDb desginated. org.Hs.eg.db will be used to map Human ENSEMBL id to gene SYMBOL.")
        }
    }
    return(AnnotationDb)
}