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#' Obtain ToilHub Info for Single Gene
#'
#' @inheritParams get_pancan_value
#' @importFrom utils data
#' @return a `tibble`
#' @export
#'
#' @examples
#' \dontrun{
#' t <- query_toil_value_df()
#' t
#' }
query_toil_value_df <- function(identifier = "TP53") {
df <- get_pancan_gene_value(identifier = identifier)
data("toil_info", package = "UCSCXenaShiny", envir = environment())
toil_info <- toil_info %>%
dplyr::left_join(dplyr::tibble(
sample = names(df$expression),
expression = df$expression
), by = "sample") %>%
dplyr::filter(!is.na(expression)) %>%
dplyr::rename(
primary_site = `_primary_site`,
sample_type = `_sample_type`,
gender = `_gender`,
study = `_study`
) %>%
dplyr::select(sample, primary_site, detailed_category, sample_type, gender, study, expression) %>%
dplyr::mutate(unit = df$unit) %>%
dplyr::as_tibble() %>%
dplyr::filter(sample_type %in% c(
"Primary Tumor", "Normal Tissue", "Primary Solid Tumor", "Solid Tissue Normal",
"Metastatic", "Cell Line", "Primary Blood Derived Cancer - Peripheral Blood",
"Primary Blood Derived Cancer - Bone Marrow", "Recurrent Blood Derived Cancer - Bone Marrow"
)) %>%
# Only keep samples with count > 100
dplyr::mutate(
sample_type = factor(sample_type, levels = c(
"Primary Tumor", "Normal Tissue", "Primary Solid Tumor", "Solid Tissue Normal",
"Metastatic", "Cell Line", "Primary Blood Derived Cancer - Peripheral Blood",
"Primary Blood Derived Cancer - Bone Marrow", "Recurrent Blood Derived Cancer - Bone Marrow"
))
)
toil_info
}
utils::globalVariables(
c(
"_primary_site",
"_sample_type",
"_gender",
"_study",
"primary_site",
"sample_type",
"gender",
"study",
"expression",
"detailed_category"
)
)
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