please_cite_biomartr <- function(mute_citation = FALSE) {
if (!mute_citation) {
cat("\n")
cat("\n")
cat("Please cite: Drost HG, Paszkowski J. Biomartr: genomic data retrieval with R. Bioinformatics (2017) 33(8): 1216-1217. doi:10.1093/bioinformatics/btw821.")
cat("\n")
}
}
organism_no_hit_message_zero <- function(organism, db) {
message(
"Unfortunatey, no entry for '",
organism,
"' was found in the '",
db,
"' database. ",
"Please consider specifying ",
paste0("'db = ", dplyr::setdiff(
db_hosts(), db
), collapse = "' or "),
"' to check whether '",organism,"' is available in these databases."
)
}
organism_no_hit_message_more_than_one <- function(organism, db) {
message("More than one entry was found for '", organism, "'.",
" Please consider to run the function 'is.genome.available()' and specify 'is.genome.available(organism = ",
organism, ", db = ",db, ", details = TRUE)'.",
" This will allow you to select the 'assembly_accession' identifier that can then be ",
"specified in all get*() functions.")
}
genomes_wrong_subset_message <- function(subset, set) {
paste0("Unfortunately, not all members of your specified subset '",
paste0(subset, collapse = ", '"),
"' could be found. Must be subset of:\n",
paste0(unique(set), collapse = ", "))
}
wrong_mart_message <- function(mart, dataset) {
dataset <- ifelse(!is.null(dataset), paste0("or dataset '", dataset,"'"), "")
paste(
"Your input mart '", mart, "'", dataset,
"could not be found. Please use getMarts() to choose from available marts."
)
}
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