R/Summaries.R

In mpi2/OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

summary.NULL <- function(object, ...) {
  message0("No summary available for NULL objects")
}
summary.OpenStatsRR <- function(object, format = "rst", ...) {
  if (!is.null(object$messages) || is.null(object)) {
    message0("Due to error(s), no summary available")
    message0(object$messages)
    stop()
  }
  summaryCore(object, procedure = "RR", format = format, ...)
}

summary.OpenStatsFE <- function(object, format = "rst", ...) {
  if (!is.null(object$messages) || is.null(object)) {
    message0("Due to error(s), no summary available")
    message0(object$messages)
    stop()
  }
  summaryCore(object, procedure = "FE", format = format, ...)
}

summary.OpenStatsMM <- function(object, format = "rst", ...) {
  if (!is.null(object$messages) || is.null(object)) {
    message0("Due to error(s), no summary available")
    message0(object$messages)
    stop()
  }
  summaryCore(object, procedure = "MM", format = format, ...)
}


summaryCore <- function(x,
                        procedure = "MM",
                        format = "rst",
                        ...) {
  message0("Working out the summary table ...")
  requireNamespace("knitr")
  vo <- OpenStatsReport(
    object = x,
    JSON = FALSE,
    ReportNullSchema = FALSE,
    RemoveNullKeys = FALSE
  )
  pasteComma2 <- function(..., NULLChar = " - ") {
    requireNamespace("rlist")
    inp <- as.list(...)
    inp <- list.clean(inp)
    if (is.null(inp) ||
      length(inp) < 1) {
      r <- NULLChar
    } else {
      r <- pasteCommaJustForSummary(
        ...,
        replaceNull   = TRUE,
        truncate      = FALSE,
        replaceNullby = NULLChar
      )
    }
    return(r)
  }
  IfoverallTableExistsThenReturnOne <- function(x, overallTableName = "Complete table") {
    if (overallTableName %in% names(x)) {
      # message0('`',overallTableName, '` found in the object')
      x <- x[[overallTableName]]
    }
    return(x)
  }
  out <- list(
    "Applied framework" = vo$`Applied method`,
    "Final model" = if (procedure %in% "MM") {
      if (!is.null(x$output$Final.Model)) {
        formula(x$output$Final.Model)
      } else {
        NULL
      }
    } else if (procedure %in% "FE") {
      RightFormula2LeftFormula(x$extra$Cleanedformula)
    } else if (procedure %in% "RR") {
      RightFormula2LeftFormula(x$extra$Cleanedformula)
    } else {
      NULL
    },
    "............................" = "............................",
    "Tested Gene" = vo$`Gp2 genotype`,
    "Reference Gene" = vo$`Gp1 genotype`,
    "............................" = "............................",
    "Sexual dimorphism detected?" = pasteComma(vo$`Genotype contribution`$`Sexual dimorphism detected`),
    "............................" = ifelse(
      procedure == "RR",
      "* Separate p-values for (Low vs NormalHigh), (LowNormal vs High) and details ",
      "............................"
    ),
    "Genotype contribution overall" = pasteComma2(IfoverallTableExistsThenReturnOne(vo$`Genotype p-value`)),
    "Genotype contribution Females" = pasteComma2(IfoverallTableExistsThenReturnOne(vo$`Sex FvKO p-value`)),
    "Genotype contribution Males" = pasteComma2(IfoverallTableExistsThenReturnOne(vo$`Sex MvKO p-value`)),
    "............................" = "............................",
    "LifeStage contribution" = pasteComma2(IfoverallTableExistsThenReturnOne(vo$`LifeStage p-value`)),
    "Genotype contribution Early" = pasteComma2(IfoverallTableExistsThenReturnOne(vo$`LifeStage EvKO p-value`)),
    "Genotype contribution Late" = pasteComma2(IfoverallTableExistsThenReturnOne(vo$`LifeStage LvKO p-value`)),
    "............................" = "............................",
    "Sex contribution" = pasteComma2(IfoverallTableExistsThenReturnOne(vo$`Sex p-value`)),
    "Body weight contribution" = pasteComma2(IfoverallTableExistsThenReturnOne(vo$`Weight p-value`))
  )
  outT <- prepareSummaryOutput(out)
  print(kable(
    outT,
    format = format,
    col.names = c("Statistic", "Value"),
    ...
  ))
  outTRemoved <- outT[!apply(outT, 1, function(x) {
    any(grepl(
      pattern = "..........",
      x = x,
      fixed = TRUE
    ))
  }), ]
  outTRemoved[outTRemoved %in% " - "] <- NA
  return(invisible(outTRemoved))
}

prepareSummaryOutput <- function(out, nullMessage = "Not applicable") {
  outT <- as.matrix(out)
  outT <- as.matrix(cbind(rownames(outT), outT))
  rownames(outT) <- NULL
  return(outT)
}


pasteCommaJustForSummary <- function(...,
                                     replaceNull = TRUE,
                                     truncate = TRUE,
                                     width = 100,
                                     trailingSpace = TRUE,
                                     replaceNullby = "NULL") {
  sep <- ifelse(trailingSpace, ", ", ",")
  if (replaceNull) {
    r <- paste(
      replaceNull(as.list(...), replaceBy = replaceNullby),
      sep      = sep,
      collapse = sep
    )
  } else {
    r <- paste(...,
      sep      = sep,
      collapse = sep
    )
  }

  if (truncate) {
    r <- truncate_text(r, width)
  }

  return(r)
}