R/hpa_summary_maker.R

In tnieuwe/HPAStainR: Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes

#' @title HPA_summary_maker
#'
#' @description Used to generate a summary file used in the second tab of the
#'  Shiny app version of HPAStainR
#'
#' @param hpa_dat The dataframe of normal tissue data downloaded by
#'  HPA_data_downloader()
#'
#' @return  A dataframe summarizing the amount of proteins tested to detected,
#'  used for the shiny app.
#'
#' @examples
#' ## Load in data from downloader
#' HPA_data <- HPA_data_downloader(save_file = FALSE)
#' ## Generate the summarized HPA file
#' hpa_summary <- HPA_summary_maker(HPA_data$hpa_dat)
#' @importFrom dplyr distinct n
#' @export
#'
#'


HPA_summary_maker <- function(hpa_dat) {
    hpa_dat_new <- hpa_dat %>% mutate(Tissue = gsub("[[:digit:]]+", "", 
        Tissue), tissue_cell = paste0(toupper(str_trim(Tissue)), " - ", 
        Cell.type)) %>% distinct() %>% group_by(tissue_cell) %>%
        summarise(proteins = n(),
                  detected = sum(!(Level %in% "Not detected"))) %>%
        mutate(det_o_test = detected/proteins)
}