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#' Load an example NanoMethResult object
#'
#' @return a NanoMethResults object
#'
#' @export
#'
#' @examples
#' nmr <- load_example_nanomethresult()
load_example_nanomethresult <- function() {
methy <- system.file(package = "NanoMethViz", "methy_subset.tsv.bgz")
sample <- c(
"B6Cast_Prom_1_bl6",
"B6Cast_Prom_1_cast",
"B6Cast_Prom_2_bl6",
"B6Cast_Prom_2_cast",
"B6Cast_Prom_3_bl6",
"B6Cast_Prom_3_cast"
)
group <- c(
"bl6",
"cast",
"bl6",
"cast",
"bl6",
"cast"
)
sample_anno <- data.frame(sample, group, stringsAsFactors = FALSE)
exon_tibble <- get_exons_mus_musculus()
NanoMethResult(methy, sample_anno, exon_tibble)
}
.get_ggplot_range_x <- function(x) {
# get x-axis range from a ggplot object
# returns c(x_min, x_max)
ggplot2::ggplot_build(x)$layout$panel_scales_x[[1]]$range$range
}
# create a list where the nth element contains the nth values of the original
# vectors
#' @importFrom stats setNames
vec_zip <- function(..., .names = NULL) {
x <- do.call(data.frame, list(..., stringsAsFactors = FALSE))
stats::setNames(split(x, seq_len(nrow(x))), .names)
}
extract_file_names <- function(x) {
fs::path_ext_remove(fs::path_file(x))
}
logit <- function(p) {
log(p / (1-p))
}
assert_has_columns <- function(x, cols) {
if (!all(cols %in% colnames(x))) {
stop(glue::glue(
"columns missing from {input}: {missing_cols}",
input = deparse(substitute(x)),
missing_cols = paste(setdiff(cols, colnames(x)), collapse = ", ")
))
}
}
timed_log <- function(...) {
time_stamp <- paste0("[", format(Sys.time(), "%F %X"), "] ")
message(time_stamp, ...)
}
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