R/sanitize.R

In AbbVie-External/OmicNavigator: Open-Source Software for 'Omic' Data Analysis and Visualization

# Sanitize the input to OmicNavigator addX() functions

sanitizeSamples <- function(samples) {
  for (i in seq_along(samples)) {
    samples[[i]] <- as.data.frame(samples[[i]])
  }

  return(samples)
}

sanitizeFeatures <- function(features) {
  for (i in seq_along(features)) {
    features[[i]] <- as.data.frame(features[[i]])
  }

  features <- lapply(features, coerceColsToCharacter)

  return(features)
}

sanitizeModels <- function(models) {
  return(models)
}

sanitizeAssays <- function(assays) {
  for (i in seq_along(assays)) {
    assays[[i]] <- as.data.frame(assays[[i]])
  }

  return(assays)
}

sanitizeTests <- function(tests) {
  return(tests)
}

sanitizeAnnotations <- function(annotations) {
  return(annotations)
}

sanitizeResults <- function(results) {
  for (i in seq_along(results)) {
    for (j in seq_along(results[[i]])) {
      results[[i]][[j]] <- as.data.frame(results[[i]][[j]])
    }
  }

  return(results)
}

sanitizeEnrichments <- function(enrichments) {
  for (i in seq_along(enrichments)) {
    for (j in seq_along(enrichments[[i]])) {
      for (k in seq_along(enrichments[[i]][[j]])) {
        enrichments[[i]][[j]][[k]] <- as.data.frame(enrichments[[i]][[j]][[k]])
      }
    }
  }

  return(enrichments)
}

sanitizeMetaFeatures <- function(metaFeatures, study = NULL) {
  for (i in seq_along(metaFeatures)) {
    metaFeatures[[i]] <- as.data.frame(metaFeatures[[i]])
  }

  metaFeatures <- lapply(metaFeatures, coerceColsToCharacter)

  return(metaFeatures)
}

sanitizePlots <- function(plots) {
  return(plots)
}

sanitizeMapping <- function(mapping) {
  return(mapping)
}

sanitizeBarcodes <- function(barcodes) {
  return(barcodes)
}

sanitizeReports <- function(reports) {
  return(reports)
}

sanitizeOverlaps <- function(overlaps) {
  for (i in seq_along(overlaps)) {
    overlaps[[i]] <- as.data.frame(overlaps[[i]])
  }

  return(overlaps)
}

sanitizeResultsLinkouts <- function(resultsLinkouts) {
  return(resultsLinkouts)
}

sanitizeEnrichmentsLinkouts <- function(enrichmentsLinkouts) {
  return(enrichmentsLinkouts)
}

sanitizeMetaFeaturesLinkouts <- function(metaFeaturesLinkouts) {
  return(metaFeaturesLinkouts)
}