R/FOP.error.check.R

In AstroPathJHU/mIFTO: mIFTO: Multiplex Immunoflourescence Titration Optimization

#########################FOP.error.check################################
#
#'Used by analysis functions to calculate to define image positivity using the
#'thresholds and connected pixel value
#'
#'define.image.positivity;
#'Created By: Benjamin Green;
#'Last Edited 09/25/2019
#'
#'Takes in an image, a threshold, and connected pixel values
#'
#' @param err.val is the image for which positivity needs to be defined
#' @return a list with three data.frames; a sn means, sn medians, and a
#' fraction of pos
#' @export
#'
FOP.error.check <- function(
    err.val) {
  print(err.val)
  err.msg <- dplyr::case_when(
    err.val ==  "Error finding IP" ~ "Could not find IP address. Using default shiny IP address.",
    #
    err.val == "Missing inputs."
    ~ "Please make sure all text boxes have inputs.\n
    Contact Sigfredo Soto at ssotodi1@jh.edu should you need any
    additional assistance.",
    #
    err.val == "Empty Directory"
    ~ "Please make sure a directory has been selected.\n
    Contact Sigfredo Soto at ssotodi1@jh.edu should you need any
    additional assistance.",
    #
    err.val == "SlideID err"
    ~ "One or more Slide Identifiers were missing in the directory.\n
    Contact Sigfredo Soto at ssotodi1@jh.edu should you need any
    additional assistance.",
    #
    err.val == "SlideID none"
    ~ "No Slide Identifiers matched files in directory.\n
    Contact Sigfredo Soto at ssotodi1@jh.edu should you need any
    additional assistance.",
    #
    err.val == "file none"
    ~ "No files found matching paramters.\n
    If positivity type is \"PPC Pixels\" please make sure
    \"coloc_data.txt\" files are present.\n
    If positivity type is \"Cells\" please make sure
    \"cell_seg_data.txt\" files are present.\n
    If positivity type is \"Tissue\" please make sure
    \"tissue_seg_data_summary.txt\" files are present.\n
    Contact Sigfredo Soto at ssotodi1@jh.edu should you need any
    additional assistance.",
    #
    grepl("session was not cleaned up properly", err.val, fixed = TRUE)
    ~ "Problems with previous run caused a read error. Please try again.",
    #
    grepl("not found in column name header", err.val, fixed = TRUE)
    ~ "Primary Opal Identifier not found in data file. This could be due to an
    incorrect Primary Opal entry or IHC being selected.\n
    Contact Sigfredo Soto at ssotodi1@jh.edu should you need any
    additional assistance.",
    #
    grepl("positivity.data", err.val, fixed = TRUE)
    ~ "Please attempt to update\\install BiocManager
    separately. \nGo into the Rstudio window where you enter commands. Make sure
    that mIFTO is closed out by hitting the little red stop button on the
    top right. Then copy and paste the following commands: \n
    install.packages('BiocManager')\n
    BiocManager::install('EBImage')\n
    Once those install, try rerunning mIFTO.",
    #
    .default = as.character(paste0(err.val, '\nPlease email this error message
                                   to Sigfredo Soto at ssotodi1@jh.edu.'))
    )
  return(err.msg)
}