R/nonInteractiveDifferentialGeneExpressionDataVisualizationFunctions.R

In guypwhunt/GEOexplorer: GEOexplorer: a webserver for gene expression analysis and visualisation

#' A Function to Plot a Venn Diagram with the
#' Number of Genes that were and were not Differentially
#' Expressed
#'
#' This function creates a venndigram containing the number
#' of genes that were and were not differentially expressed
#' @param dT An object that summarises if each gene is
#' unregulated, down regulated or has a similar level of
#' expression which can be obtained from the
#' calculateDifferentialGeneExpressionSummary() function
#' @keywords GEO
#' @import limma
#' @examples
#' # Get the GEO data for all platforms
#' geoAccessionCode <- "GSE18388"
#' allGset <- getGeoObject(geoAccessionCode)
#'
#' # Extract platforms
#' platforms <- extractPlatforms(allGset)
#' platform <- platforms[1]
#'
#' # Extract the GEO2R data from the specified platform
#' gsetData <- extractPlatformGset(allGset, platform)
#'
#' # Extract expression data
#' expressionData <- extractExpressionData(gsetData)
#'
#' # Apply log transformation to expression data if necessary
#' logTransformation <- "Auto-Detect"
#' dataInput <- calculateLogTransformation(expressionData,
#' logTransformation)
#'
#' # Perform KNN transformation on log expression data if necessary
#' knnDataInput <- calculateKnnImpute(dataInput, "Yes")
#'
#' # Extract experimental condition/sample names
#' columnNames <- extractSampleNames(expressionData)
#'
#' # Define Groups
#' numberOfColumns <- length(columnNames)
#' numberOfColumns <- numberOfColumns + 1
#' halfNumberOfColumns <- ceiling(numberOfColumns/2)
#' i <- 0
#'
#' group1 <- c()
#' group2 <- c()
#'
#' for (name in columnNames) {
#' if (i < halfNumberOfColumns) {
#' group1 <- c(group1, name)
#' i <- i +1
#' } else {
#' group2 <- c(group2, name)
#' i <- i +1
#' }
#' }
#'
#' # Select columns in group2
#' column2 <- calculateExclusiveColumns(columnNames, group1)
#'
#' # Calculate gsms
#' gsms <- calculateEachGroupsSamples(columnNames,group1, group2)
#'
#' # Convert P value adjustment
#' pValueAdjustment <- "Benjamini & Hochberg (False discovery rate)"
#' adjustment <- convertAdjustment(pValueAdjustment)
#'
#' # Get fit 2
#' limmaPrecisionWeights <- "Yes"
#' forceNormalization <- "Yes"
#' fit2 <- calculateDifferentialGeneExpression(gsms,
#' limmaPrecisionWeights, forceNormalization, gsetData,
#' knnDataInput)
#'
#' # Summarize test results as "up", "down" or "not expressed"
#' significanceLevelCutOff <- 0.05
#' dT <- calculateDifferentialGeneExpressionSummary(fit2,
#' adjustment, significanceLevelCutOff)
#'
#' # Non-Interactive Venn diagram
#' fig <- nonInteractiveVennDiagramPlot(dT)
#'
#' @author Guy Hunt
#' @noRd
#' @seealso [calculateDifferentialGeneExpressionSummary()]
#' for differential gene expression summary object
nonInteractiveVennDiagramPlot <- function(dT) {
  fig <- vennDiagram(dT, circle.col = palette())
  return(fig)
}

#' A Function to Create a QQ Plot of the Quantiles of a
#' Data Sample Against the Theoretical Quantiles of a
#' Student's T Distribution from Differential Gene
#' Expression Analysis
#'
#' This function allows you to plot a QQ plot of the
#' quantiles of a data sample against the theoretical
#' quantiles of a Student's t distribution from differential
#' gene expression analysis
#' @param fit2 An object containing the results of differential
#' gene expression analysis which can be obtained from the
#' calculateDifferentialGeneExpression() function
#' @keywords GEO
#' @import limma
#' @examples
#' # Get the GEO data for all platforms
#' geoAccessionCode <- "GSE18388"
#' allGset <- getGeoObject(geoAccessionCode)
#'
#' # Extract platforms
#' platforms <- extractPlatforms(allGset)
#' platform <- platforms[1]
#'
#' # Extract the GEO2R data from the specified platform
#' gsetData <- extractPlatformGset(allGset, platform)
#'
#' # Extract expression data
#' expressionData <- extractExpressionData(gsetData)
#'
#' # Apply log transformation to expression data if necessary
#' logTransformation <- "Auto-Detect"
#' dataInput <- calculateLogTransformation(expressionData,
#' logTransformation)
#'
#' # Perform KNN transformation on log expression data if necessary
#' knnDataInput <- calculateKnnImpute(dataInput, "Yes")
#'
#' # Extract experimental condition/sample names
#' columnNames <- extractSampleNames(expressionData)
#'
#' # Define Groups
#' numberOfColumns <- length(columnNames)
#' numberOfColumns <- numberOfColumns + 1
#' halfNumberOfColumns <- ceiling(numberOfColumns/2)
#' i <- 0
#'
#' group1 <- c()
#' group2 <- c()
#'
#' for (name in columnNames) {
#'   if (i < halfNumberOfColumns) {
#'     group1 <- c(group1, name)
#'     i <- i +1
#' } else {
#'     group2 <- c(group2, name)
#'     i <- i +1
#'   }
#' }
#'
#' # Select columns in group2
#' column2 <- calculateExclusiveColumns(columnNames, group1)
#'
#' # Calculate gsms
#' gsms <- calculateEachGroupsSamples(columnNames,group1, group2)
#'
#' # Convert P value adjustment
#' pValueAdjustment <- "Benjamini & Hochberg (False discovery rate)"
#' adjustment <- convertAdjustment(pValueAdjustment)
#'
#' # Get fit 2
#' limmaPrecisionWeights <- "Yes"
#' forceNormalization <- "Yes"
#' fit2 <- calculateDifferentialGeneExpression(gsms,
#' limmaPrecisionWeights, forceNormalization, gsetData,
#' knnDataInput)
#'
#' # Non-Interactive Q-Q plot
#' fig <- nonInteractiveQQPlot(fit2)
#'
#' @author Guy Hunt
#' @noRd
#' @seealso [calculateDifferentialGeneExpression()]
#' for differential gene expression object
nonInteractiveQQPlot <- function(fit2) {
  # create Q-Q plot for t-statistic
  t.good <- which(!is.na(fit2$F)) # filter out bad probes
  fig <-
    qqt(fit2$t[t.good], fit2$df.total[t.good], main = "Moderated t statistic")
  return(fig)
}

#' A Function to Create a Volcano Plot of the Statistical
#' Significance (-log10 P Value) Versus Magnitude of Change
#' (log2 Fold Change) from Differential Gene Expression Analysis
#'
#' This function allows you to plot a volcano plot of the
#' statistical significance (-log10 P value) versus magnitude
#' of change (log2 fold change) from differential gene
#' expression analysis
#' @param fit2 An object containing the results of differential
#'  gene expression analysis which can be obtained from the
#'  calculateDifferentialGeneExpression() function
#' @param dT An object that summarises if each gene is
#' unregulated, down regulated or has a similar level of
#' expression which can be obtained from the
#' calculateDifferentialGeneExpressionSummary() function
#' @param ct A integer indicating the column to select
#' from the dT object
#' @keywords GEO
#' @import limma
#' @examples
#' # Get the GEO data for all platforms
#' geoAccessionCode <- "GSE18388"
#' allGset <- getGeoObject(geoAccessionCode)
#'
#' # Extract platforms
#' platforms <- extractPlatforms(allGset)
#' platform <- platforms[1]
#'
#' # Extract the GEO2R data from the specified platform
#' gsetData <- extractPlatformGset(allGset, platform)
#'
#' # Extract expression data
#' expressionData <- extractExpressionData(gsetData)
#'
#' # Apply log transformation to expression data if necessary
#' logTransformation <- "Auto-Detect"
#' dataInput <- calculateLogTransformation(expressionData,
#' logTransformation)
#'
#' # Perform KNN transformation on log expression data if necessary
#' knnDataInput <- calculateKnnImpute(dataInput, "Yes")
#'
#' # Extract experimental condition/sample names
#' columnNames <- extractSampleNames(expressionData)
#'
#' # Define Groups
#' numberOfColumns <- length(columnNames)
#' numberOfColumns <- numberOfColumns + 1
#' halfNumberOfColumns <- ceiling(numberOfColumns/2)
#' i <- 0
#'
#' group1 <- c()
#' group2 <- c()
#'
#' for (name in columnNames) {
#'   if (i < halfNumberOfColumns) {
#'     group1 <- c(group1, name)
#'     i <- i +1
#'   } else {
#'     group2 <- c(group2, name)
#'     i <- i +1
#'   }
#' }
#'
#' # Select columns in group2
#' column2 <- calculateExclusiveColumns(columnNames, group1)
#'
#' # Calculate gsms
#' gsms <- calculateEachGroupsSamples(columnNames,group1, group2)
#'
#' # Convert P value adjustment
#' pValueAdjustment <- "Benjamini & Hochberg (False discovery rate)"
#' adjustment <- convertAdjustment(pValueAdjustment)
#'
#' # Get fit 2
#' limmaPrecisionWeights <- "Yes"
#' forceNormalization <- "Yes"
#' fit2 <- calculateDifferentialGeneExpression(gsms,
#' limmaPrecisionWeights, forceNormalization, gsetData,
#' knnDataInput)
#'
#' # Summarize test results as "up", "down" or "not expressed"
#' significanceLevelCutOff <- 0.05
#' dT <- calculateDifferentialGeneExpressionSummary(fit2,
#' adjustment, significanceLevelCutOff)
#' ct <- 1
#'
#' # Non-Interactive volcano plot (log P-value vs log fold change)
#'fig <- nonInteractiveVolcanoPlot(fit2, dT, ct)
#'
#' @author Guy Hunt
#' @noRd
#' @seealso [calculateDifferentialGeneExpressionSummary()]
#' for differential gene expression summary object,
#' [calculateDifferentialGeneExpression()]
#' for differential gene expression object
nonInteractiveVolcanoPlot <- function(fit2, dT, ct) {
  # volcano plot (log P-value vs log fold change)
  colnames(fit2) # list contrast names
  fig <- volcanoplot(
    fit2,
    coef = ct,
    main = colnames(fit2)[ct],
    pch = 20,
    highlight = length(which(dT[, ct] != 0)),
    names = rep('+', nrow(fit2))
  )
  return(fig)
}

#' A Function to Create a Mean Difference Plot of the
#' log2 Fold Change Versus Average log2 Expression Values
#' from Differential Gene Expression Analysis
#'
#' This function allows you to plot a mean difference plot
#' of the log2 fold change versus average log2 expression
#' values from differential gene expression analysis
#' @param fit2 An object containing the results of differential
#' gene expression analysis which can be obtained from the
#' calculateDifferentialGeneExpression() function
#' @param dT An object that summarises if each gene is
#' unregulated, down regulated or has a similar level of
#' expression which can be obtained from the
#' calculateDifferentialGeneExpressionSummary() function
#' @param ct A integer indicating the column to select from
#' the dT object
#' @keywords GEO
#' @import limma
#' @examples
#' # Get the GEO data for all platforms
#' geoAccessionCode <- "GSE18388"
#' allGset <- getGeoObject(geoAccessionCode)
#'
#' # Extract platforms
#' platforms <- extractPlatforms(allGset)
#' platform <- platforms[1]
#'
#' # Extract the GEO2R data from the specified platform
#' gsetData <- extractPlatformGset(allGset, platform)
#'
#' # Extract expression data
#' expressionData <- extractExpressionData(gsetData)
#'
#' # Apply log transformation to expression data if necessary
#' logTransformation <- "Auto-Detect"
#' dataInput <- calculateLogTransformation(expressionData,
#' logTransformation)
#'
#' # Perform KNN transformation on log expression data if necessary
#' knnDataInput <- calculateKnnImpute(dataInput, "Yes")
#'
#' # Extract experimental condition/sample names
#' columnNames <- extractSampleNames(expressionData)
#'
#' # Define Groups
#' numberOfColumns <- length(columnNames)
#' numberOfColumns <- numberOfColumns + 1
#' halfNumberOfColumns <- ceiling(numberOfColumns/2)
#' i <- 0
#'
#' group1 <- c()
#' group2 <- c()
#'
#' for (name in columnNames) {
#'   if (i < halfNumberOfColumns) {
#'     group1 <- c(group1, name)
#'     i <- i +1
#'   } else {
#'     group2 <- c(group2, name)
#'     i <- i +1
#'   }
#' }
#'
#' # Select columns in group2
#' column2 <- calculateExclusiveColumns(columnNames, group1)
#'
#' # Calculate gsms
#' gsms <- calculateEachGroupsSamples(columnNames,group1, group2)
#'
#' # Convert P value adjustment
#' pValueAdjustment <- "Benjamini & Hochberg (False discovery rate)"
#' adjustment <- convertAdjustment(pValueAdjustment)
#'
#' # Get fit 2
#' limmaPrecisionWeights <- "Yes"
#' forceNormalization <- "Yes"
#' fit2 <- calculateDifferentialGeneExpression(gsms,
#' limmaPrecisionWeights, forceNormalization, gsetData,
#' knnDataInput)
#'
#' # Summarize test results as "up", "down" or "not expressed"
#' significanceLevelCutOff <- 0.05
#' dT <- calculateDifferentialGeneExpressionSummary(fit2,
#' adjustment, significanceLevelCutOff)
#' ct <- 1
#'
#' # MD plot (log fold change vs mean log expression)
#' fig <- noninteractiveMeanDifferencePlot(fit2, dT, ct)
#'
#' @author Guy Hunt
#' @noRd
#' @seealso [calculateDifferentialGeneExpressionSummary()]
#' for differential gene expression summary object,
#' [calculateDifferentialGeneExpression()]
#' for differential gene expression object
noninteractiveMeanDifferencePlot <- function(fit2, dT, ct) {
  # MD plot (log fold change vs mean log expression)
  # highlight statistically significant (p-adj < 0.05) probes
  fig <-
    plotMD(
      fit2,
      column = ct,
      status = dT[, ct],
      legend = FALSE,
      pch = 20,
      cex = 1
    )
  abline(h = 0)
  return(fig)
}

#' A Function to Create a Histogram of the P values from
#' Differential Gene Expression Analysis
#'
#' This function allows you to plot a histogram of the
#' P values from differential gene expression analysis
#' @param fit2 An object containing the results of
#' differential gene expression analysis which can be
#' obtained from the calculateDifferentialGeneExpression()
#' function
#' @param adjustment A character string containing the
#' adjustment to P-values
#' @keywords GEO
#' @import limma
#' @examples
#' #' # Get the GEO data for all platforms
#' geoAccessionCode <- "GSE18388"
#' allGset <- getGeoObject(geoAccessionCode)
#'
#' # Extract platforms
#' platforms <- extractPlatforms(allGset)
#' platform <- platforms[1]
#'
#' # Extract the GEO2R data from the specified platform
#' gsetData <- extractPlatformGset(allGset, platform)
#'
#' # Extract expression data
#' expressionData <- extractExpressionData(gsetData)
#'
#' # Apply log transformation to expression data if necessary
#' logTransformation <- "Auto-Detect"
#' dataInput <- calculateLogTransformation(expressionData,
#' logTransformation)
#'
#' # Perform KNN transformation on log expression data if necessary
#' knnDataInput <- calculateKnnImpute(dataInput, "Yes")
#'
#' # Extract experimental condition/sample names
#' columnNames <- extractSampleNames(expressionData)
#'
#' # Define Groups
#' numberOfColumns <- length(columnNames)
#' numberOfColumns <- numberOfColumns + 1
#' halfNumberOfColumns <- ceiling(numberOfColumns/2)
#' i <- 0
#'
#' group1 <- c()
#' group2 <- c()
#'
#' for (name in columnNames) {
#'   if (i < halfNumberOfColumns) {
#'     group1 <- c(group1, name)
#'     i <- i +1
#'   } else {
#'     group2 <- c(group2, name)
#'     i <- i +1
#'   }
#' }
#'
#' # Select columns in group2
#' column2 <- calculateExclusiveColumns(columnNames, group1)
#'
#' # Calculate gsms
#' gsms <- calculateEachGroupsSamples(columnNames,group1, group2)
#'
#' # Convert P value adjustment
#' pValueAdjustment <- "Benjamini & Hochberg (False discovery rate)"
#' adjustment <- convertAdjustment(pValueAdjustment)
#'
#' # Get fit 2
#' limmaPrecisionWeights <- "Yes"
#' forceNormalization <- "Yes"
#' fit2 <- calculateDifferentialGeneExpression(gsms,
#' limmaPrecisionWeights, forceNormalization, gsetData,
#' knnDataInput)
#'
#' # Summarize test results as "up", "down" or "not expressed"
#' significanceLevelCutOff <- 0.05
#' dT <- calculateDifferentialGeneExpressionSummary(fit2,
#' adjustment, significanceLevelCutOff)
#' ct <- 1
#'
#' # Non-Interactive Histogram
#' fig <- nonInteractiveHistogramPlot(fit2, adjustment)
#'
#' fig <- nonInteractiveHistogramPlot(fit2, adjustment)
#' @author Guy Hunt
#' @noRd
#' @seealso [calculateDifferentialGeneExpression()]
#' for differential gene expression object
nonInteractiveHistogramPlot <- function(fit2, adjustment) {
  tT2 <- topTable(fit2,
                  adjust.method = adjustment,
                  sort.by = "B",
                  number = Inf)
  fig <-
    hist(
      tT2$adj.P.Val,
      col = "grey",
      border = "white",
      xlab = "P-adj",
      ylab = "Number of genes",
      main = "P-adj value distribution"
    )
  return(fig)
}