R/zzz.R

In whtns/seuratTools: Tools for Managing Seurat Objects

# global reference to scvelo (will be initialized in .onLoad)
#
scvelo <- NULL
matplotlib <- NULL
pyplot <- NULL
.onLoad <- function(libname, pkgname) {
    # reticulate::configure_environment(pkgname, force = TRUE)
    # use superassignment to update global reference to scvelo
    scvelo <<- reticulate::import("scvelo", delay_load = TRUE)
    matplotlib <<- reticulate::import("matplotlib", convert = TRUE)
    matplotlib$use("Agg", force = TRUE)
    pyplot <<- reticulate::import("matplotlib.pyplot", delay_load = TRUE)
    # human_gene_transcript_seu <- RunUMAP(human_gene_transcript_seu, dims = 1:30)
}

install_scvelo <- function(method = "auto", conda = "auto") {
    reticulate::py_install("scvelo", method = method, conda = conda, pip = TRUE)
    reticulate::py_install("matplotlib", method = method, conda = conda)
}