R/samplesMetricMap.R
In DarioS/ClassifyR: A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
#' Plot a Grid of Sample-wise Predictive Metrics
#'
#' A grid of coloured tiles is drawn. There is one column for each sample and
#' one row for each cross-validation result.
#'
#' The names of \code{results} determine the row names that will be in the
#' plot. The length of \code{metricColours} determines how many bins the metric
#' values will be discretised to.
#'
#' @aliases samplesMetricMap samplesMetricMap,list-method
#' samplesMetricMap,matrix-method
#' @param results A list of \code{\link{ClassifyResult}} objects. Could also be
#' a matrix of pre-calculated metrics, for backwards compatibility.
#' @param classes If \code{results} is a matrix, this is a factor vector of the
#' same length as the number of columns that \code{results} has.
#' @param comparison Default: \code{"auto"}. The aspect of the experimental
#' design to compare. Can be any characteristic that all results share.
#' @param metric Default: \code{"auto"}. The name of the
#' performance measure or "auto". If the results are classification then
#' sample accuracy will be displayed. Otherwise, the results would be survival risk
#' predictions and then a sample C-index will be displayed. Valid values are \code{"Sample Error"},
#' \code{"Sample Error"} or \code{"Sample C-index"}. If the metric is not stored in the
#' results list, the performance metric will be calculated automatically.
#' @param featureValues If not NULL, can be a named factor or named numeric
#' vector specifying some variable of interest to plot above the heatmap.
#' @param featureName A label describing the information in
#' \code{featureValues}. It must be specified if \code{featureValues} is.
#' @param metricColours If the outcome is categorical, a list of vectors of colours
#' for metric levels for each class. If the outcome is numeric, such as a risk score,
#' then a single vector of colours for the metric levels for all samples.
#' @param classColours Either a vector of colours for class levels if both
#' classes should have same colour, or a list of length 2, with each component
#' being a vector of the same length. The vector has the colour gradient for
#' each class.
#' @param groupColours A vector of colours for group levels. Only useful if
#' \code{featureValues} is not NULL.
#' @param fontSizes A vector of length 5. The first number is the size of the
#' title. The second number is the size of the axes titles. The third number
#' is the size of the axes values. The fourth number is the size of the
#' legends' titles. The fifth number is the font size of the legend labels.
#' @param mapHeight Height of the map, relative to the height of the class
#' colour bar.
#' @param title The title to place above the plot.
#' @param showLegends Logical. IF FALSE, the legend is not drawn.
#' @param xAxisLabel The name plotted for the x-axis. NULL suppresses label.
#' @param showXtickLabels Logical. IF FALSE, the x-axis labels are hidden.
#' @param showYtickLabels Logical. IF FALSE, the y-axis labels are hidden.
#' @param yAxisLabel The name plotted for the y-axis. NULL suppresses label.
#' @param legendSize The size of the boxes in the legends.
#' @param ... Parameters not used by the \code{ClassifyResult} method that does
#' list-packaging but used by the main \code{list} method.
#' @return A grob is returned that can be drawn on a graphics device.
#' @author Dario Strbenac
#' @examples
#'
#' predicted <- DataFrame(sample = LETTERS[sample(10, 100, replace = TRUE)],
#' class = rep(c("Healthy", "Cancer"), each = 50))
#' actual <- factor(rep(c("Healthy", "Cancer"), each = 5), levels = c("Healthy", "Cancer"))
#' features <- sapply(1:100, function(index) paste(sample(LETTERS, 3), collapse = ''))
#' result1 <- ClassifyResult(DataFrame(characteristic = c("Data Set", "Selection Name", "Classifier Name",
#' "Cross-validation"),
#' value = c("Example", "t-test", "Differential Expression", "2 Permutations, 2 Folds")),
#' LETTERS[1:10], features, list(1:100), list(sample(10, 10)),
#' list(function(oracle){}), NULL, predicted, actual)
#' predicted[, "class"] <- sample(predicted[, "class"])
#' result2 <- ClassifyResult(DataFrame(characteristic = c("Data Set", "Selection Name", "Classifier Name",
#' "Cross-validation"),
#' value = c("Example", "Bartlett Test", "Differential Variability", "2 Permutations, 2 Folds")),
#' LETTERS[1:10], features, list(1:100), list(sample(10, 10)),
#' list(function(oracle){}), NULL, predicted, actual)
#' result1 <- calcCVperformance(result1)
#' result2 <- calcCVperformance(result2)
#' groups <- factor(rep(c("Male", "Female"), length.out = 10))
#' names(groups) <- LETTERS[1:10]
#' cholesterol <- c(4.0, 5.5, 3.9, 4.9, 5.7, 7.1, 7.9, 8.0, 8.5, 7.2)
#' names(cholesterol) <- LETTERS[1:10]
#'
#' wholePlot <- samplesMetricMap(list(Gene = result1, Protein = result2))
#' wholePlot <- samplesMetricMap(list(Gene = result1, Protein = result2),
#' featureValues = groups, featureName = "Gender")
#' wholePlot <- samplesMetricMap(list(Gene = result1, Protein = result2),
#' featureValues = cholesterol, featureName = "Cholesterol")
#'
#' @export
#' @usage NULL
setGeneric("samplesMetricMap", function(results, ...)
standardGeneric("samplesMetricMap"))
#' @rdname samplesMetricMap
#' @export
setMethod("samplesMetricMap", "ClassifyResult", function(results, ...) {
samplesMetricMap(list(assay = results), ...)
})
#' @rdname samplesMetricMap
#' @export
setMethod("samplesMetricMap", "list",
function(results,
comparison = "auto",
metric = "auto",
featureValues = NULL, featureName = NULL,
metricColours = list(c("#FFFFFF", "#CFD1F2", "#9FA3E5", "#6F75D8", "#3F48CC"),
c("#FFFFFF", "#E1BFC4", "#C37F8A", "#A53F4F", "#880015")),
classColours = c("#3F48CC", "#880015"), groupColours = c("darkgreen", "yellow2"),
fontSizes = c(24, 16, 12, 12, 12),
mapHeight = 4, title = "auto",
showLegends = TRUE, xAxisLabel = "Sample Name", showXtickLabels = TRUE,
yAxisLabel = "Analysis", showYtickLabels = TRUE, legendSize = grid::unit(1, "lines"))
{
if(!requireNamespace("ggplot2", quietly = TRUE))
stop("The package 'ggplot2' could not be found. Please install it.")
if(!requireNamespace("gridExtra", quietly = TRUE))
stop("The package 'gridExtra' could not be found. Please install it.")
if(!requireNamespace("gtable", quietly = TRUE))
stop("The package 'gtable' could not be found. Please install it.")
characteristicsCounts <- table(unlist(lapply(results, function(result) result@characteristics[["characteristic"]])))
if(comparison == "auto")
{
if(max(characteristicsCounts) == length(results))
{ # Choose a characteristic which varies the most across the results.
candidates <- names(characteristicsCounts)[characteristicsCounts == length(results)]
allCharacteristics <- do.call(rbind, lapply(results, function(result) result@characteristics))
distinctValues <- by(allCharacteristics[, "value"], allCharacteristics[, "characteristic"], function(values) length(unique(values)))
comparison <- names(distinctValues)[which.max(distinctValues)][1]
} else {
stop("No characteristic is present for all results but must be.")
}
}
isSurvival <- "risk" %in% colnames(results[[1]]@predictions)
validMetrics <- c("Sample Error", "Sample Accuracy", "Sample C-index")
if(metric == "auto")
metric <- ifelse(isSurvival, "Sample C-index", "Sample Accuracy")
else
if(!metric %in% validMetrics) stop("metric must be one of ", validMetrics, " but is ", metric, '.')
if(title == "auto") title <- switch(metric, `Sample Error` = "Error Comparison", `Sample Accuracy` = "Accuracy Comparison", `Sample C-index` = "Risk Score Comparison")
if(isSurvival && is.list(metricColours)) metricColours <- metricColours[[1]]
metricText <- gsub("Sample ", '', metric) # For legend labelling.
if(showXtickLabels == FALSE && xAxisLabel == "Sample Name") xAxisLabel <- "Sample"
resultsWithComparison <- sum(sapply(results, function(result) any(result@characteristics[, "characteristic"] == comparison)))
if(resultsWithComparison < length(results))
stop("Not all results have comparison characteristic ", comparison, ' but need to.')
if(comparison == "Cross-validation")
compareFactor <- sapply(results, function(result) .validationText(result))
else
compareFactor <- sapply(results, function(result) {
useRow <- result@characteristics[, "characteristic"] == comparison
result@characteristics[useRow, "value"]
})
metrics <- unlist(lapply(results, function(result)
if(!is.null(result@performance)) names(result@performance)))
namesCounts <- table(metrics)
commonNames <- names(namesCounts)[namesCounts == length(results)]
if(!metric %in% commonNames)
{
warning(paste(metric, "not found in all elements of results. Calculating it now."))
results <- lapply(results, function(result) calcCVperformance(result, metric))
}
if(!is.null(featureValues) && is.null(featureName))
stop("featureValues is specified by featureNames isn't. Specify both.")
if(!is.null(featureValues) && is.null(names(featureValues)))
stop("featureValues vector must be named with sample IDs.")
comparisonValuesCounts <- table(compareFactor)
if(any(comparisonValuesCounts > 1))
stop("Some classification results have same the comparison value. Check that each
clasification result is distinctive for the comparison type specified by
'comparison'.")
nColours <- if(is.list(metricColours)) length(metricColours[[1]]) else length(metricColours)
metricBinEnds <- seq(0, 1, 1/nColours)
metricValues <- lapply(results, function(result)
{
sampleMetricValues <- result@performance[[metric]]
cut(sampleMetricValues, metricBinEnds, include.lowest = TRUE)
})
if(metric != "Sample C-index")
{
knownClasses <- actualOutcome(results[[1]])
classedMetricValues <- lapply(metricValues, function(metricSet)
{
metricSet <- factor(paste(knownClasses, metricSet, sep = ','),
levels = c(t(outer(levels(knownClasses), levels(metricSet), paste, sep = ','))))
})
} else {knownClasses <- NULL}
meanMetricCategory <- colMeans(do.call(rbind, metricValues))
if(metric == "Sample Error")
meanMetricCategory <- meanMetricCategory * -1 # For sorting purposes.
if(is.null(featureValues))
{
if(metric != "Sample C-index") # Sort within each class.
ordering <- order(knownClasses, meanMetricCategory)
else # Sort all samples together.
ordering <- order(meanMetricCategory)
} else {
featureValues <- featureValues[match(sampleNames(results[[1]]), names(featureValues))]
#featureValues <- featureValues[match(results[[1]]@performance[[metric]], names(featureValues))]
if(metric != "Sample C-index") # Sort within each class.
ordering <- order(knownClasses, featureValues, meanMetricCategory)
else # Sort all samples together.
ordering <- order(featureValues, meanMetricCategory)
}
if(metric != "Sample C-index")
knownClasses <- knownClasses[ordering]
if(!is.null(featureValues))
featureValues <- featureValues[ordering]
metricValues <- lapply(metricValues, function(resultMetricValues) resultMetricValues[ordering])
if(metric != "Sample C-index") classedMetricValues <- lapply(classedMetricValues, function(resultmetricValues) resultmetricValues[ordering])
plotData <- data.frame(name = factor(rep(sampleNames(results[[1]])[ordering], length(results)), levels = sampleNames(results[[1]])[ordering]),
type = factor(rep(compareFactor, sapply(metricValues, length)), levels = rev(compareFactor)),
Metric = unlist(metricValues))
if(metric != "Sample C-index") plotData <- cbind(plotData, class = rep(knownClasses, length(results)))
originalLegends <- showLegends
originalmetricColours <- metricColours
showLegends <- FALSE
if(is.list(metricColours))
{
metricColours <- unlist(metricColours)
plotData[, "Metric"] <- unlist(classedMetricValues)
}
if(metric != "Sample C-index")
{
classData <- data.frame(Class = knownClasses)
classesPlot <- ggplot2::ggplot(classData, ggplot2::aes(1:length(knownClasses), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(values = classColours) + ggplot2::geom_tile(ggplot2::aes(fill = Class)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0.2, 0, 0.01, 0), "npc"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
}
if(!is.null(featureValues))
{
if(is.factor(featureValues))
{
featureValuesData <- data.frame(Group = featureValues)
featureValuesPlot <- ggplot2::ggplot(featureValuesData, ggplot2::aes(1:length(featureValues), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(name = featureName, values = groupColours) + ggplot2::geom_tile(ggplot2::aes(fill = Group)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 0, 0), "npc"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
} else # Numeric data about the samples.
{
featureValuesData <- data.frame(measurements = featureValues, Class = 1)
if(metric != "Sample C-index") featureValuesData[, "Class"] <- knownClasses
featureValuesPlot <- ggplot2::ggplot(featureValuesData, environment = environment()) +
ggplot2::geom_point(ggplot2::aes(x = 1:length(featureValues), y = measurements, colour = Class)) +
ggplot2::scale_x_continuous(expand = ggplot2::expansion(add = 0.5), breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_continuous(breaks = c(min(featureValues), max(featureValues))) +
ggplot2::labs(x = featureName, y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 1, 0), "lines"),
axis.text = ggplot2::element_text(colour = "black"),
axis.title.x = ggplot2::element_text(size = fontSizes[4]),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize, panel.background = ggplot2::element_blank(),
panel.border = ggplot2::element_rect(colour = "black", fill = "transparent")
)
if(metric != "Sample C-index")
featureValuesPlot <- featureValuesPlot + ggplot2::scale_colour_manual(values = classColours)
}
}
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(values = metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 1, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
if(metric != "Sample C-index")
classGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(classesPlot))
metricGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
if(!is.null(featureValues))
featureValuesGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(featureValuesPlot))
if(!is.null(featureValues))
{
if(metric != "Sample C-index")
commonWidth <- grid::unit.pmax(classGrob[["widths"]], metricGrob[["widths"]], featureValuesGrob[["widths"]])
else
commonWidth <- grid::unit.pmax(metricGrob[["widths"]], featureValuesGrob[["widths"]])
} else {
if(metric != "Sample C-index")
commonWidth <- grid::unit.pmax(classGrob[["widths"]], metricGrob[["widths"]])
else
commonWidth <- metricGrob[["widths"]]
}
if(metric != "Sample C-index") classGrob[["widths"]] <- commonWidth
metricGrob[["widths"]] <- commonWidth
if(!is.null(featureValues))
featureValuesGrob[["widths"]] <- commonWidth
if(originalLegends == TRUE)
{
showLegends <- TRUE
metricColours <- originalmetricColours
if(metric != "Sample C-index")
{ classesPlot <- ggplot2::ggplot(classData, ggplot2::aes(1:length(knownClasses), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(values = classColours) + ggplot2::geom_tile(ggplot2::aes(fill = Class)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(knownClasses))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0.2, 0, 0.01, 0), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
classGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(classesPlot))
}
if(!is.null(featureValues) && is.factor(featureValues))
{
featureValuesPlot <- ggplot2::ggplot(featureValuesData, ggplot2::aes(1:length(featureValues), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(name = featureName, values = groupColours) + ggplot2::geom_tile(ggplot2::aes(fill = Group)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 0, 0), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
featureValuesGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(featureValuesPlot))
} else {featureValuesGrobUnused <- grid::grob()}
plotData[, "Metric"] <- unlist(metricValues)
classLegend <- NULL
if(is.list(metricColours) && metric != "Sample C-index")
classLegend <- paste(levels(knownClasses)[1], NULL)
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(name = paste(classLegend, metricText, sep = ''),
values = if(is.list(metricColours)) metricColours[[1]] else metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 0, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
metricGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
if(!is.null(featureValues) && is.factor(featureValues))
{
if(metric != "Sample C-index")
commonWidth <- grid::unit.pmax(classGrobUnused[["widths"]], metricGrobUnused[["widths"]], featureValuesGrobUnused[["widths"]])
else
commonWidth <- grid::unit.pmax(metricGrobUnused[["widths"]], featureValuesGrobUnused[["widths"]])
} else {
if(metric != "Sample C-index")
commonWidth <- grid::unit.pmax(classGrobUnused[["widths"]], metricGrobUnused[["widths"]])
else
commonWidth <- metricGrobUnused[["widths"]]
}
metricGrobUnused[["widths"]] <- commonWidth
if(metric != "Sample C-index")
classGrobUnused[["widths"]] <- commonWidth
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesGrobUnused[["widths"]] <- commonWidth
if(metric != "Sample C-index")
classLegend <- classGrobUnused[["grobs"]][[which(sapply(classGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesLegend <- featureValuesGrobUnused[["grobs"]][[which(sapply(featureValuesGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
else
featureValuesLegend <- grid::grob()
if(showLegends == TRUE)
firstLegend <- metricGrobUnused[["grobs"]][[which(sapply(metricGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(name = paste(levels(knownClasses)[2], metricText),
values = if(is.list(metricColours)) metricColours[[2]] else metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 1, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
metricGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
metricGrobUnused[["widths"]] <- commonWidth
secondLegend <- metricGrobUnused[["grobs"]][[which(sapply(metricGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
}
if(showLegends == TRUE)
{
annosHeight <- grid::unit(1 / (mapHeight + 1), "npc")
if(!is.null(featureValues) && is.factor(featureValues))
{
if(metric != "Sample C-index")
legendWidth <- max(sum(classLegend[["widths"]]), sum(firstLegend[["widths"]]), sum(featureValuesLegend[["widths"]]))
else
legendWidth <- max(sum(firstLegend[["widths"]]), sum(featureValuesLegend[["widths"]]))
} else {
if(metric != "Sample C-index")
legendWidth <- max(sum(classLegend[["widths"]]), sum(firstLegend[["widths"]]))
else
legendWidth <- sum(firstLegend[["widths"]])
}
featureValuesHeight <- grid::unit(0, "cm")
if(!is.null(featureValues))
{
if(is.factor(featureValues))
featureValuesHeight <- featureValuesLegend[["heights"]][3]
else
featureValuesHeight <- annosHeight
}
if(is.list(metricColours))
legendHeight <- (grid::unit(1, "npc") - featureValuesHeight) * (mapHeight / (mapHeight + 1) / 2)
else
legendHeight <- (grid::unit(1, "npc") - featureValuesHeight) * (mapHeight / (mapHeight + 1))
widths <- grid::unit.c(unit(1, "npc") - legendWidth, legendWidth)
if(metric != "Sample C-index") classesHeight <- unit(1 / (mapHeight + 1), "npc") else classesHeight <- unit(0, "npc")
heights <- grid::unit.c(classesHeight, featureValuesHeight, legendHeight)
if(is.list(metricColours))
{
heights <- grid::unit.c(heights, legendHeight)
} else # Greyscale legend.
{
heights <- grid::unit.c(heights, unit(1, "npc") - legendHeight - featureValuesHeight - grid::unit(1 / (mapHeight + 1), "npc"))
}
}
else
{
widths <- grid::unit(1, "npc")
heights <- grid::unit.c(grid::unit(1 / (mapHeight + 1), "npc"), featureValuesHeight, grid::unit(1, "npc") - featureValuesHeight - grid::unit(1 / (mapHeight + 1), "npc"))
}
if(metric != "Sample C-index")
classLegend[["vp"]][["valid.just"]] <- c(0.7, 0.5)
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesLegend[["vp"]][["valid.just"]] <- c(0.7, 0.33)
grobTable <- gtable::gtable(widths, heights)
if(metric != "Sample C-index")
grobTable <- gtable::gtable_add_grob(grobTable, classGrob, 1, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, grid::grob(), 1, 1)
if(!is.null(featureValues))
grobTable <- gtable::gtable_add_grob(grobTable, featureValuesGrob, 2, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, grid::grob(), 2, 1)
if(showLegends == TRUE)
{
if(is.list(metricColours))
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1, 4, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1, 3, 1)
} else
{
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1)
}
if(showLegends == TRUE)
{
if(metric != "Sample C-index")
grobTable <- gtable::gtable_add_grob(grobTable, classLegend, 1, 2)
grobTable <- gtable::gtable_add_grob(grobTable, featureValuesLegend, 2, 2)
}
if(showLegends == TRUE && !is.list(metricColours))
{
firstLegend[["vp"]][["valid.just"]] <- c(0.62, 0.5)
grobTable <- gtable::gtable_add_grob(grobTable, firstLegend, 3, 2)
}
if(showLegends == TRUE && is.list(metricColours))
{
firstLegend[["vp"]][["valid.just"]] <- c(0.62, 0.5)
secondLegend[["vp"]][["valid.just"]] <- c(0.62, 0.4)
grobTable <- gtable::gtable_add_grob(grobTable, firstLegend, 3, 2)
grobTable <- gtable::gtable_add_grob(grobTable, secondLegend, 4, 2)
}
wholePlot <- gridExtra::arrangeGrob(grobTable, top = grid::textGrob(title, vjust = 0.5, gp = grid::gpar(fontsize = fontSizes[1])))
grid::grid.draw(wholePlot)
wholePlot
})
#' @rdname samplesMetricMap
#' @export
setMethod("samplesMetricMap", "matrix",
function(results, classes,
metric = c("Sample Error", "Sample Accuracy"),
featureValues = NULL, featureName = NULL,
metricColours = list(c("#3F48CC", "#6F75D8", "#9FA3E5", "#CFD1F2", "#FFFFFF"),
c("#880015", "#A53F4F", "#C37F8A", "#E1BFC4", "#FFFFFF")),
classColours = c("#3F48CC", "#880015"), groupColours = c("darkgreen", "yellow2"),
fontSizes = c(24, 16, 12, 12, 12),
mapHeight = 4, title = "Error Comparison", showLegends = TRUE, xAxisLabel = "Sample Name", showXtickLabels = TRUE,
yAxisLabel = "Analysis", showYtickLabels = TRUE, legendSize = grid::unit(1, "lines"))
{
if(!requireNamespace("ggplot2", quietly = TRUE))
stop("The package 'ggplot2' could not be found. Please install it.")
if(!requireNamespace("gridExtra", quietly = TRUE))
stop("The package 'gridExtra' could not be found. Please install it.")
if(!requireNamespace("gtable", quietly = TRUE))
stop("The package 'gtable' could not be found. Please install it.")
metric <- match.arg(metric)
metricText <- switch(metric, `Sample Error` = "Error", `Sample Accuracy` = "Accuracy")
if(!is.null(featureValues) && is.null(featureName))
stop("featureValues is specified by featureNames isn't. Specify both.")
nColours <- if(is.list(metricColours)) length(metricColours[[1]]) else length(metricColours)
metricBinEnds <- seq(0, 1, 1/nColours)
knownClasses <- classes
sampleIDs <- colnames(results)
characteristic <- rownames(results)
results <- as.list(as.data.frame(t(results)))
metricValues <- lapply(results, function(result)
{
cut(result, metricBinEnds, include.lowest = TRUE)
})
classedMetricValues <- lapply(metricValues, function(metricSet)
{
metricSet <- factor(paste(knownClasses, metricSet, sep = ','),
levels = c(t(outer(levels(knownClasses), levels(metricSet), paste, sep = ','))))
})
meanMetricCategory <- colMeans(do.call(rbind, metricValues))
if(metric == "Sample Error")
meanMetricCategory <- meanMetricCategory * -1 # For sorting purposes.
if(is.null(featureValues))
{
ordering <- order(knownClasses, meanMetricCategory)
} else {
featureValues <- featureValues[match(sampleNames(results[[1]]), names(featureValues))]
ordering <- order(knownClasses, featureValues, meanMetricCategory)
}
knownClasses <- knownClasses[ordering]
if(!is.null(featureValues))
featureValues <- featureValues[ordering]
metricValues <- lapply(metricValues, function(resultmetricValues) resultmetricValues[ordering])
classedMetricValues <- lapply(classedMetricValues, function(resultmetricValues) resultmetricValues[ordering])
sampleIDs <- sampleIDs[ordering]
plotData <- data.frame(name = factor(rep(sampleIDs, length(characteristic)), levels = sampleIDs),
type = factor(rep(characteristic, each = length(sampleIDs)), levels = rev(characteristic)),
class = rep(knownClasses, length(characteristic)),
Metric = unlist(metricValues))
originalLegends <- showLegends
originalmetricColours <- metricColours
showLegends <- FALSE
if(is.list(metricColours))
{
metricColours <- unlist(metricColours)
plotData[, "Metric"] <- unlist(classedMetricValues)
}
classData <- data.frame(Class = knownClasses)
classesPlot <- ggplot2::ggplot(classData, ggplot2::aes(1:length(knownClasses), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(values = classColours) + ggplot2::geom_tile(ggplot2::aes(fill = Class)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(knownClasses))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0.2, 0, 0.01, 0), "npc"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
if(!is.null(featureValues))
{
if(is.factor(featureValues))
{
featureValuesData <- data.frame(Group = featureValues)
featureValuesPlot <- ggplot2::ggplot(featureValuesData, ggplot2::aes(1:length(featureValues), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(name = featureName, values = groupColours) + ggplot2::geom_tile(ggplot2::aes(fill = Group)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 0, 0), "npc"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
} else # Numeric data about the samples.
{
featureValuesData <- data.frame(Class = knownClasses, measurements = featureValues)
featureValuesPlot <- ggplot2::ggplot(featureValuesData, environment = environment()) +
ggplot2::geom_point(ggplot2::aes(x = 1:length(featureValues), y = measurements, colour = Class)) +
ggplot2::scale_colour_manual(values = classColours) +
ggplot2::scale_x_continuous(breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_continuous(breaks = c(min(featureValues), max(featureValues))) +
ggplot2::labs(x = featureName, y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 1, 0), "lines"),
axis.text = ggplot2::element_text(colour = "black"),
axis.title.x = ggplot2::element_text(size = fontSizes[4]),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize, panel.background = ggplot2::element_blank(),
panel.border = ggplot2::element_rect(colour = "black", fill = "transparent")
)
}
}
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(values = metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 1, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
classGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(classesPlot))
metricGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
if(!is.null(featureValues))
featureValuesGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(featureValuesPlot))
if(!is.null(featureValues))
commonWidth <- grid::unit.pmax(classGrob[["widths"]], metricGrob[["widths"]], featureValuesGrob[["widths"]])
else
commonWidth <- grid::unit.pmax(classGrob[["widths"]], metricGrob[["widths"]])
classGrob[["widths"]] <- commonWidth
metricGrob[["widths"]] <- commonWidth
if(!is.null(featureValues))
featureValuesGrob[["widths"]] <- commonWidth
if(originalLegends == TRUE)
{
showLegends <- TRUE
metricColours <- originalmetricColours
classesPlot <- ggplot2::ggplot(classData, ggplot2::aes(1:length(knownClasses), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(values = classColours) + ggplot2::geom_tile(ggplot2::aes(fill = Class)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(knownClasses))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0.2, 0, 0.01, 0), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
classGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(classesPlot))
if(!is.null(featureValues) && is.factor(featureValues))
{
featureValuesPlot <- ggplot2::ggplot(featureValuesData, ggplot2::aes(1:length(featureValues), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(name = featureName, values = groupColours) + ggplot2::geom_tile(ggplot2::aes(fill = Group)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 0, 0), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
featureValuesGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(featureValuesPlot))
} else {featureValuesGrobUnused <- grid::grob()}
plotData[, "Metric"] <- unlist(metricValues)
classLegend <- NULL
if(is.list(metricColours))
classLegend <- paste(levels(knownClasses)[1], NULL)
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(name = paste(classLegend, metricText, sep = ''),
values = if(is.list(metricColours)) metricColours[[1]] else metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 0, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
metricGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
if(!is.null(featureValues) && is.factor(featureValues))
commonWidth <- grid::unit.pmax(classGrobUnused[["widths"]], metricGrobUnused[["widths"]], featureValuesGrobUnused[["widths"]])
else
commonWidth <- grid::unit.pmax(classGrobUnused[["widths"]], metricGrobUnused[["widths"]])
metricGrobUnused[["widths"]] <- commonWidth
classGrobUnused[["widths"]] <- commonWidth
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesGrobUnused[["widths"]] <- commonWidth
classLegend <- classGrobUnused[["grobs"]][[which(sapply(classGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesLegend <- featureValuesGrobUnused[["grobs"]][[which(sapply(featureValuesGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
else
featureValuesLegend <- grid::grob()
if(showLegends == TRUE)
firstLegend <- metricGrobUnused[["grobs"]][[which(sapply(metricGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(name = paste(levels(knownClasses)[2], metricText),
values = if(is.list(metricColours)) metricColours[[2]] else metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 1, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
metricGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
metricGrobUnused[["widths"]] <- commonWidth
secondLegend <- metricGrobUnused[["grobs"]][[which(sapply(metricGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
}
if(showLegends == TRUE)
{
classesHeight <- grid::unit(1 / (mapHeight + 1), "npc")
if(!is.null(featureValues) && is.factor(featureValues))
legendWidth <- max(sum(classLegend[["widths"]]), sum(firstLegend[["widths"]]), sum(featureValuesLegend[["widths"]]))
else
legendWidth <- max(sum(classLegend[["widths"]]), sum(firstLegend[["widths"]]))
featureValuesHeight <- grid::unit(0, "cm")
if(!is.null(featureValues))
{
if(is.factor(featureValues))
featureValuesHeight <- featureValuesLegend[["heights"]][3]
else
featureValuesHeight <- classesHeight
}
if(is.list(metricColours))
legendHeight <- (grid::unit(1, "npc") - featureValuesHeight) * (mapHeight / (mapHeight + 1) / 2)
else
legendHeight <- (grid::unit(1, "npc") - featureValuesHeight) * (mapHeight / (mapHeight + 1))
widths <- grid::unit.c(unit(1, "npc") - legendWidth, legendWidth)
heights <- grid::unit.c(unit(1 / (mapHeight + 1), "npc"), featureValuesHeight, legendHeight)
if(is.list(metricColours))
{
heights <- grid::unit.c(heights, legendHeight)
} else # Greyscale legend.
{
heights <- grid::unit.c(heights, unit(1, "npc") - legendHeight - featureValuesHeight - grid::unit(1 / (mapHeight + 1), "npc"))
}
}
else
{
widths <- grid::unit(1, "npc")
heights <- grid::unit.c(grid::unit(1 / (mapHeight + 1), "npc"), featureValuesHeight, grid::unit(1, "npc") - featureValuesHeight - grid::unit(1 / (mapHeight + 1), "npc"))
}
classLegend[["vp"]][["valid.just"]] <- c(0.7, 0.5)
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesLegend[["vp"]][["valid.just"]] <- c(0.7, 0.33)
grobTable <- gtable::gtable(widths, heights)
grobTable <- gtable::gtable_add_grob(grobTable, classGrob, 1, 1)
if(!is.null(featureValues))
grobTable <- gtable::gtable_add_grob(grobTable, featureValuesGrob, 2, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, grid::grob(), 2, 1)
if(showLegends == TRUE)
{
if(is.list(metricColours))
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1, 4, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1, 3, 1)
} else
{
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1)
}
if(showLegends == TRUE)
{
grobTable <- gtable::gtable_add_grob(grobTable, classLegend, 1, 2)
grobTable <- gtable::gtable_add_grob(grobTable, featureValuesLegend, 2, 2)
}
if(showLegends == TRUE && !is.list(metricColours))
{
firstLegend[["vp"]][["valid.just"]] <- c(0.62, 0.5)
grobTable <- gtable::gtable_add_grob(grobTable, firstLegend, 3, 2)
}
if(showLegends == TRUE && is.list(metricColours))
{
firstLegend[["vp"]][["valid.just"]] <- c(0.62, 0.5)
secondLegend[["vp"]][["valid.just"]] <- c(0.62, 0.4)
grobTable <- gtable::gtable_add_grob(grobTable, firstLegend, 3, 2)
grobTable <- gtable::gtable_add_grob(grobTable, secondLegend, 4, 2)
}
wholePlot <- gridExtra::arrangeGrob(grobTable, top = grid::textGrob(title, vjust = 0.5, gp = grid::gpar(fontsize = fontSizes[1])))
grid::grid.draw(wholePlot)
wholePlot
})
DarioS/ClassifyR documentation built on Dec. 19, 2024, 8:22 p.m.
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#' Plot a Grid of Sample-wise Predictive Metrics
#'
#' A grid of coloured tiles is drawn. There is one column for each sample and
#' one row for each cross-validation result.
#'
#' The names of \code{results} determine the row names that will be in the
#' plot. The length of \code{metricColours} determines how many bins the metric
#' values will be discretised to.
#'
#' @aliases samplesMetricMap samplesMetricMap,list-method
#' samplesMetricMap,matrix-method
#' @param results A list of \code{\link{ClassifyResult}} objects. Could also be
#' a matrix of pre-calculated metrics, for backwards compatibility.
#' @param classes If \code{results} is a matrix, this is a factor vector of the
#' same length as the number of columns that \code{results} has.
#' @param comparison Default: \code{"auto"}. The aspect of the experimental
#' design to compare. Can be any characteristic that all results share.
#' @param metric Default: \code{"auto"}. The name of the
#' performance measure or "auto". If the results are classification then
#' sample accuracy will be displayed. Otherwise, the results would be survival risk
#' predictions and then a sample C-index will be displayed. Valid values are \code{"Sample Error"},
#' \code{"Sample Error"} or \code{"Sample C-index"}. If the metric is not stored in the
#' results list, the performance metric will be calculated automatically.
#' @param featureValues If not NULL, can be a named factor or named numeric
#' vector specifying some variable of interest to plot above the heatmap.
#' @param featureName A label describing the information in
#' \code{featureValues}. It must be specified if \code{featureValues} is.
#' @param metricColours If the outcome is categorical, a list of vectors of colours
#' for metric levels for each class. If the outcome is numeric, such as a risk score,
#' then a single vector of colours for the metric levels for all samples.
#' @param classColours Either a vector of colours for class levels if both
#' classes should have same colour, or a list of length 2, with each component
#' being a vector of the same length. The vector has the colour gradient for
#' each class.
#' @param groupColours A vector of colours for group levels. Only useful if
#' \code{featureValues} is not NULL.
#' @param fontSizes A vector of length 5. The first number is the size of the
#' title. The second number is the size of the axes titles. The third number
#' is the size of the axes values. The fourth number is the size of the
#' legends' titles. The fifth number is the font size of the legend labels.
#' @param mapHeight Height of the map, relative to the height of the class
#' colour bar.
#' @param title The title to place above the plot.
#' @param showLegends Logical. IF FALSE, the legend is not drawn.
#' @param xAxisLabel The name plotted for the x-axis. NULL suppresses label.
#' @param showXtickLabels Logical. IF FALSE, the x-axis labels are hidden.
#' @param showYtickLabels Logical. IF FALSE, the y-axis labels are hidden.
#' @param yAxisLabel The name plotted for the y-axis. NULL suppresses label.
#' @param legendSize The size of the boxes in the legends.
#' @param ... Parameters not used by the \code{ClassifyResult} method that does
#' list-packaging but used by the main \code{list} method.
#' @return A grob is returned that can be drawn on a graphics device.
#' @author Dario Strbenac
#' @examples
#'
#' predicted <- DataFrame(sample = LETTERS[sample(10, 100, replace = TRUE)],
#' class = rep(c("Healthy", "Cancer"), each = 50))
#' actual <- factor(rep(c("Healthy", "Cancer"), each = 5), levels = c("Healthy", "Cancer"))
#' features <- sapply(1:100, function(index) paste(sample(LETTERS, 3), collapse = ''))
#' result1 <- ClassifyResult(DataFrame(characteristic = c("Data Set", "Selection Name", "Classifier Name",
#' "Cross-validation"),
#' value = c("Example", "t-test", "Differential Expression", "2 Permutations, 2 Folds")),
#' LETTERS[1:10], features, list(1:100), list(sample(10, 10)),
#' list(function(oracle){}), NULL, predicted, actual)
#' predicted[, "class"] <- sample(predicted[, "class"])
#' result2 <- ClassifyResult(DataFrame(characteristic = c("Data Set", "Selection Name", "Classifier Name",
#' "Cross-validation"),
#' value = c("Example", "Bartlett Test", "Differential Variability", "2 Permutations, 2 Folds")),
#' LETTERS[1:10], features, list(1:100), list(sample(10, 10)),
#' list(function(oracle){}), NULL, predicted, actual)
#' result1 <- calcCVperformance(result1)
#' result2 <- calcCVperformance(result2)
#' groups <- factor(rep(c("Male", "Female"), length.out = 10))
#' names(groups) <- LETTERS[1:10]
#' cholesterol <- c(4.0, 5.5, 3.9, 4.9, 5.7, 7.1, 7.9, 8.0, 8.5, 7.2)
#' names(cholesterol) <- LETTERS[1:10]
#'
#' wholePlot <- samplesMetricMap(list(Gene = result1, Protein = result2))
#' wholePlot <- samplesMetricMap(list(Gene = result1, Protein = result2),
#' featureValues = groups, featureName = "Gender")
#' wholePlot <- samplesMetricMap(list(Gene = result1, Protein = result2),
#' featureValues = cholesterol, featureName = "Cholesterol")
#'
#' @export
#' @usage NULL
setGeneric("samplesMetricMap", function(results, ...)
standardGeneric("samplesMetricMap"))
#' @rdname samplesMetricMap
#' @export
setMethod("samplesMetricMap", "ClassifyResult", function(results, ...) {
samplesMetricMap(list(assay = results), ...)
})
#' @rdname samplesMetricMap
#' @export
setMethod("samplesMetricMap", "list",
function(results,
comparison = "auto",
metric = "auto",
featureValues = NULL, featureName = NULL,
metricColours = list(c("#FFFFFF", "#CFD1F2", "#9FA3E5", "#6F75D8", "#3F48CC"),
c("#FFFFFF", "#E1BFC4", "#C37F8A", "#A53F4F", "#880015")),
classColours = c("#3F48CC", "#880015"), groupColours = c("darkgreen", "yellow2"),
fontSizes = c(24, 16, 12, 12, 12),
mapHeight = 4, title = "auto",
showLegends = TRUE, xAxisLabel = "Sample Name", showXtickLabels = TRUE,
yAxisLabel = "Analysis", showYtickLabels = TRUE, legendSize = grid::unit(1, "lines"))
{
if(!requireNamespace("ggplot2", quietly = TRUE))
stop("The package 'ggplot2' could not be found. Please install it.")
if(!requireNamespace("gridExtra", quietly = TRUE))
stop("The package 'gridExtra' could not be found. Please install it.")
if(!requireNamespace("gtable", quietly = TRUE))
stop("The package 'gtable' could not be found. Please install it.")
characteristicsCounts <- table(unlist(lapply(results, function(result) result@characteristics[["characteristic"]])))
if(comparison == "auto")
{
if(max(characteristicsCounts) == length(results))
{ # Choose a characteristic which varies the most across the results.
candidates <- names(characteristicsCounts)[characteristicsCounts == length(results)]
allCharacteristics <- do.call(rbind, lapply(results, function(result) result@characteristics))
distinctValues <- by(allCharacteristics[, "value"], allCharacteristics[, "characteristic"], function(values) length(unique(values)))
comparison <- names(distinctValues)[which.max(distinctValues)][1]
} else {
stop("No characteristic is present for all results but must be.")
}
}
isSurvival <- "risk" %in% colnames(results[[1]]@predictions)
validMetrics <- c("Sample Error", "Sample Accuracy", "Sample C-index")
if(metric == "auto")
metric <- ifelse(isSurvival, "Sample C-index", "Sample Accuracy")
else
if(!metric %in% validMetrics) stop("metric must be one of ", validMetrics, " but is ", metric, '.')
if(title == "auto") title <- switch(metric, `Sample Error` = "Error Comparison", `Sample Accuracy` = "Accuracy Comparison", `Sample C-index` = "Risk Score Comparison")
if(isSurvival && is.list(metricColours)) metricColours <- metricColours[[1]]
metricText <- gsub("Sample ", '', metric) # For legend labelling.
if(showXtickLabels == FALSE && xAxisLabel == "Sample Name") xAxisLabel <- "Sample"
resultsWithComparison <- sum(sapply(results, function(result) any(result@characteristics[, "characteristic"] == comparison)))
if(resultsWithComparison < length(results))
stop("Not all results have comparison characteristic ", comparison, ' but need to.')
if(comparison == "Cross-validation")
compareFactor <- sapply(results, function(result) .validationText(result))
else
compareFactor <- sapply(results, function(result) {
useRow <- result@characteristics[, "characteristic"] == comparison
result@characteristics[useRow, "value"]
})
metrics <- unlist(lapply(results, function(result)
if(!is.null(result@performance)) names(result@performance)))
namesCounts <- table(metrics)
commonNames <- names(namesCounts)[namesCounts == length(results)]
if(!metric %in% commonNames)
{
warning(paste(metric, "not found in all elements of results. Calculating it now."))
results <- lapply(results, function(result) calcCVperformance(result, metric))
}
if(!is.null(featureValues) && is.null(featureName))
stop("featureValues is specified by featureNames isn't. Specify both.")
if(!is.null(featureValues) && is.null(names(featureValues)))
stop("featureValues vector must be named with sample IDs.")
comparisonValuesCounts <- table(compareFactor)
if(any(comparisonValuesCounts > 1))
stop("Some classification results have same the comparison value. Check that each
clasification result is distinctive for the comparison type specified by
'comparison'.")
nColours <- if(is.list(metricColours)) length(metricColours[[1]]) else length(metricColours)
metricBinEnds <- seq(0, 1, 1/nColours)
metricValues <- lapply(results, function(result)
{
sampleMetricValues <- result@performance[[metric]]
cut(sampleMetricValues, metricBinEnds, include.lowest = TRUE)
})
if(metric != "Sample C-index")
{
knownClasses <- actualOutcome(results[[1]])
classedMetricValues <- lapply(metricValues, function(metricSet)
{
metricSet <- factor(paste(knownClasses, metricSet, sep = ','),
levels = c(t(outer(levels(knownClasses), levels(metricSet), paste, sep = ','))))
})
} else {knownClasses <- NULL}
meanMetricCategory <- colMeans(do.call(rbind, metricValues))
if(metric == "Sample Error")
meanMetricCategory <- meanMetricCategory * -1 # For sorting purposes.
if(is.null(featureValues))
{
if(metric != "Sample C-index") # Sort within each class.
ordering <- order(knownClasses, meanMetricCategory)
else # Sort all samples together.
ordering <- order(meanMetricCategory)
} else {
featureValues <- featureValues[match(sampleNames(results[[1]]), names(featureValues))]
#featureValues <- featureValues[match(results[[1]]@performance[[metric]], names(featureValues))]
if(metric != "Sample C-index") # Sort within each class.
ordering <- order(knownClasses, featureValues, meanMetricCategory)
else # Sort all samples together.
ordering <- order(featureValues, meanMetricCategory)
}
if(metric != "Sample C-index")
knownClasses <- knownClasses[ordering]
if(!is.null(featureValues))
featureValues <- featureValues[ordering]
metricValues <- lapply(metricValues, function(resultMetricValues) resultMetricValues[ordering])
if(metric != "Sample C-index") classedMetricValues <- lapply(classedMetricValues, function(resultmetricValues) resultmetricValues[ordering])
plotData <- data.frame(name = factor(rep(sampleNames(results[[1]])[ordering], length(results)), levels = sampleNames(results[[1]])[ordering]),
type = factor(rep(compareFactor, sapply(metricValues, length)), levels = rev(compareFactor)),
Metric = unlist(metricValues))
if(metric != "Sample C-index") plotData <- cbind(plotData, class = rep(knownClasses, length(results)))
originalLegends <- showLegends
originalmetricColours <- metricColours
showLegends <- FALSE
if(is.list(metricColours))
{
metricColours <- unlist(metricColours)
plotData[, "Metric"] <- unlist(classedMetricValues)
}
if(metric != "Sample C-index")
{
classData <- data.frame(Class = knownClasses)
classesPlot <- ggplot2::ggplot(classData, ggplot2::aes(1:length(knownClasses), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(values = classColours) + ggplot2::geom_tile(ggplot2::aes(fill = Class)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0.2, 0, 0.01, 0), "npc"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
}
if(!is.null(featureValues))
{
if(is.factor(featureValues))
{
featureValuesData <- data.frame(Group = featureValues)
featureValuesPlot <- ggplot2::ggplot(featureValuesData, ggplot2::aes(1:length(featureValues), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(name = featureName, values = groupColours) + ggplot2::geom_tile(ggplot2::aes(fill = Group)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 0, 0), "npc"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
} else # Numeric data about the samples.
{
featureValuesData <- data.frame(measurements = featureValues, Class = 1)
if(metric != "Sample C-index") featureValuesData[, "Class"] <- knownClasses
featureValuesPlot <- ggplot2::ggplot(featureValuesData, environment = environment()) +
ggplot2::geom_point(ggplot2::aes(x = 1:length(featureValues), y = measurements, colour = Class)) +
ggplot2::scale_x_continuous(expand = ggplot2::expansion(add = 0.5), breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_continuous(breaks = c(min(featureValues), max(featureValues))) +
ggplot2::labs(x = featureName, y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 1, 0), "lines"),
axis.text = ggplot2::element_text(colour = "black"),
axis.title.x = ggplot2::element_text(size = fontSizes[4]),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize, panel.background = ggplot2::element_blank(),
panel.border = ggplot2::element_rect(colour = "black", fill = "transparent")
)
if(metric != "Sample C-index")
featureValuesPlot <- featureValuesPlot + ggplot2::scale_colour_manual(values = classColours)
}
}
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(values = metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 1, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
if(metric != "Sample C-index")
classGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(classesPlot))
metricGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
if(!is.null(featureValues))
featureValuesGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(featureValuesPlot))
if(!is.null(featureValues))
{
if(metric != "Sample C-index")
commonWidth <- grid::unit.pmax(classGrob[["widths"]], metricGrob[["widths"]], featureValuesGrob[["widths"]])
else
commonWidth <- grid::unit.pmax(metricGrob[["widths"]], featureValuesGrob[["widths"]])
} else {
if(metric != "Sample C-index")
commonWidth <- grid::unit.pmax(classGrob[["widths"]], metricGrob[["widths"]])
else
commonWidth <- metricGrob[["widths"]]
}
if(metric != "Sample C-index") classGrob[["widths"]] <- commonWidth
metricGrob[["widths"]] <- commonWidth
if(!is.null(featureValues))
featureValuesGrob[["widths"]] <- commonWidth
if(originalLegends == TRUE)
{
showLegends <- TRUE
metricColours <- originalmetricColours
if(metric != "Sample C-index")
{ classesPlot <- ggplot2::ggplot(classData, ggplot2::aes(1:length(knownClasses), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(values = classColours) + ggplot2::geom_tile(ggplot2::aes(fill = Class)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(knownClasses))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0.2, 0, 0.01, 0), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
classGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(classesPlot))
}
if(!is.null(featureValues) && is.factor(featureValues))
{
featureValuesPlot <- ggplot2::ggplot(featureValuesData, ggplot2::aes(1:length(featureValues), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(name = featureName, values = groupColours) + ggplot2::geom_tile(ggplot2::aes(fill = Group)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 0, 0), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
featureValuesGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(featureValuesPlot))
} else {featureValuesGrobUnused <- grid::grob()}
plotData[, "Metric"] <- unlist(metricValues)
classLegend <- NULL
if(is.list(metricColours) && metric != "Sample C-index")
classLegend <- paste(levels(knownClasses)[1], NULL)
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(name = paste(classLegend, metricText, sep = ''),
values = if(is.list(metricColours)) metricColours[[1]] else metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 0, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
metricGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
if(!is.null(featureValues) && is.factor(featureValues))
{
if(metric != "Sample C-index")
commonWidth <- grid::unit.pmax(classGrobUnused[["widths"]], metricGrobUnused[["widths"]], featureValuesGrobUnused[["widths"]])
else
commonWidth <- grid::unit.pmax(metricGrobUnused[["widths"]], featureValuesGrobUnused[["widths"]])
} else {
if(metric != "Sample C-index")
commonWidth <- grid::unit.pmax(classGrobUnused[["widths"]], metricGrobUnused[["widths"]])
else
commonWidth <- metricGrobUnused[["widths"]]
}
metricGrobUnused[["widths"]] <- commonWidth
if(metric != "Sample C-index")
classGrobUnused[["widths"]] <- commonWidth
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesGrobUnused[["widths"]] <- commonWidth
if(metric != "Sample C-index")
classLegend <- classGrobUnused[["grobs"]][[which(sapply(classGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesLegend <- featureValuesGrobUnused[["grobs"]][[which(sapply(featureValuesGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
else
featureValuesLegend <- grid::grob()
if(showLegends == TRUE)
firstLegend <- metricGrobUnused[["grobs"]][[which(sapply(metricGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(name = paste(levels(knownClasses)[2], metricText),
values = if(is.list(metricColours)) metricColours[[2]] else metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 1, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
metricGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
metricGrobUnused[["widths"]] <- commonWidth
secondLegend <- metricGrobUnused[["grobs"]][[which(sapply(metricGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
}
if(showLegends == TRUE)
{
annosHeight <- grid::unit(1 / (mapHeight + 1), "npc")
if(!is.null(featureValues) && is.factor(featureValues))
{
if(metric != "Sample C-index")
legendWidth <- max(sum(classLegend[["widths"]]), sum(firstLegend[["widths"]]), sum(featureValuesLegend[["widths"]]))
else
legendWidth <- max(sum(firstLegend[["widths"]]), sum(featureValuesLegend[["widths"]]))
} else {
if(metric != "Sample C-index")
legendWidth <- max(sum(classLegend[["widths"]]), sum(firstLegend[["widths"]]))
else
legendWidth <- sum(firstLegend[["widths"]])
}
featureValuesHeight <- grid::unit(0, "cm")
if(!is.null(featureValues))
{
if(is.factor(featureValues))
featureValuesHeight <- featureValuesLegend[["heights"]][3]
else
featureValuesHeight <- annosHeight
}
if(is.list(metricColours))
legendHeight <- (grid::unit(1, "npc") - featureValuesHeight) * (mapHeight / (mapHeight + 1) / 2)
else
legendHeight <- (grid::unit(1, "npc") - featureValuesHeight) * (mapHeight / (mapHeight + 1))
widths <- grid::unit.c(unit(1, "npc") - legendWidth, legendWidth)
if(metric != "Sample C-index") classesHeight <- unit(1 / (mapHeight + 1), "npc") else classesHeight <- unit(0, "npc")
heights <- grid::unit.c(classesHeight, featureValuesHeight, legendHeight)
if(is.list(metricColours))
{
heights <- grid::unit.c(heights, legendHeight)
} else # Greyscale legend.
{
heights <- grid::unit.c(heights, unit(1, "npc") - legendHeight - featureValuesHeight - grid::unit(1 / (mapHeight + 1), "npc"))
}
}
else
{
widths <- grid::unit(1, "npc")
heights <- grid::unit.c(grid::unit(1 / (mapHeight + 1), "npc"), featureValuesHeight, grid::unit(1, "npc") - featureValuesHeight - grid::unit(1 / (mapHeight + 1), "npc"))
}
if(metric != "Sample C-index")
classLegend[["vp"]][["valid.just"]] <- c(0.7, 0.5)
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesLegend[["vp"]][["valid.just"]] <- c(0.7, 0.33)
grobTable <- gtable::gtable(widths, heights)
if(metric != "Sample C-index")
grobTable <- gtable::gtable_add_grob(grobTable, classGrob, 1, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, grid::grob(), 1, 1)
if(!is.null(featureValues))
grobTable <- gtable::gtable_add_grob(grobTable, featureValuesGrob, 2, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, grid::grob(), 2, 1)
if(showLegends == TRUE)
{
if(is.list(metricColours))
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1, 4, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1, 3, 1)
} else
{
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1)
}
if(showLegends == TRUE)
{
if(metric != "Sample C-index")
grobTable <- gtable::gtable_add_grob(grobTable, classLegend, 1, 2)
grobTable <- gtable::gtable_add_grob(grobTable, featureValuesLegend, 2, 2)
}
if(showLegends == TRUE && !is.list(metricColours))
{
firstLegend[["vp"]][["valid.just"]] <- c(0.62, 0.5)
grobTable <- gtable::gtable_add_grob(grobTable, firstLegend, 3, 2)
}
if(showLegends == TRUE && is.list(metricColours))
{
firstLegend[["vp"]][["valid.just"]] <- c(0.62, 0.5)
secondLegend[["vp"]][["valid.just"]] <- c(0.62, 0.4)
grobTable <- gtable::gtable_add_grob(grobTable, firstLegend, 3, 2)
grobTable <- gtable::gtable_add_grob(grobTable, secondLegend, 4, 2)
}
wholePlot <- gridExtra::arrangeGrob(grobTable, top = grid::textGrob(title, vjust = 0.5, gp = grid::gpar(fontsize = fontSizes[1])))
grid::grid.draw(wholePlot)
wholePlot
})
#' @rdname samplesMetricMap
#' @export
setMethod("samplesMetricMap", "matrix",
function(results, classes,
metric = c("Sample Error", "Sample Accuracy"),
featureValues = NULL, featureName = NULL,
metricColours = list(c("#3F48CC", "#6F75D8", "#9FA3E5", "#CFD1F2", "#FFFFFF"),
c("#880015", "#A53F4F", "#C37F8A", "#E1BFC4", "#FFFFFF")),
classColours = c("#3F48CC", "#880015"), groupColours = c("darkgreen", "yellow2"),
fontSizes = c(24, 16, 12, 12, 12),
mapHeight = 4, title = "Error Comparison", showLegends = TRUE, xAxisLabel = "Sample Name", showXtickLabels = TRUE,
yAxisLabel = "Analysis", showYtickLabels = TRUE, legendSize = grid::unit(1, "lines"))
{
if(!requireNamespace("ggplot2", quietly = TRUE))
stop("The package 'ggplot2' could not be found. Please install it.")
if(!requireNamespace("gridExtra", quietly = TRUE))
stop("The package 'gridExtra' could not be found. Please install it.")
if(!requireNamespace("gtable", quietly = TRUE))
stop("The package 'gtable' could not be found. Please install it.")
metric <- match.arg(metric)
metricText <- switch(metric, `Sample Error` = "Error", `Sample Accuracy` = "Accuracy")
if(!is.null(featureValues) && is.null(featureName))
stop("featureValues is specified by featureNames isn't. Specify both.")
nColours <- if(is.list(metricColours)) length(metricColours[[1]]) else length(metricColours)
metricBinEnds <- seq(0, 1, 1/nColours)
knownClasses <- classes
sampleIDs <- colnames(results)
characteristic <- rownames(results)
results <- as.list(as.data.frame(t(results)))
metricValues <- lapply(results, function(result)
{
cut(result, metricBinEnds, include.lowest = TRUE)
})
classedMetricValues <- lapply(metricValues, function(metricSet)
{
metricSet <- factor(paste(knownClasses, metricSet, sep = ','),
levels = c(t(outer(levels(knownClasses), levels(metricSet), paste, sep = ','))))
})
meanMetricCategory <- colMeans(do.call(rbind, metricValues))
if(metric == "Sample Error")
meanMetricCategory <- meanMetricCategory * -1 # For sorting purposes.
if(is.null(featureValues))
{
ordering <- order(knownClasses, meanMetricCategory)
} else {
featureValues <- featureValues[match(sampleNames(results[[1]]), names(featureValues))]
ordering <- order(knownClasses, featureValues, meanMetricCategory)
}
knownClasses <- knownClasses[ordering]
if(!is.null(featureValues))
featureValues <- featureValues[ordering]
metricValues <- lapply(metricValues, function(resultmetricValues) resultmetricValues[ordering])
classedMetricValues <- lapply(classedMetricValues, function(resultmetricValues) resultmetricValues[ordering])
sampleIDs <- sampleIDs[ordering]
plotData <- data.frame(name = factor(rep(sampleIDs, length(characteristic)), levels = sampleIDs),
type = factor(rep(characteristic, each = length(sampleIDs)), levels = rev(characteristic)),
class = rep(knownClasses, length(characteristic)),
Metric = unlist(metricValues))
originalLegends <- showLegends
originalmetricColours <- metricColours
showLegends <- FALSE
if(is.list(metricColours))
{
metricColours <- unlist(metricColours)
plotData[, "Metric"] <- unlist(classedMetricValues)
}
classData <- data.frame(Class = knownClasses)
classesPlot <- ggplot2::ggplot(classData, ggplot2::aes(1:length(knownClasses), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(values = classColours) + ggplot2::geom_tile(ggplot2::aes(fill = Class)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(knownClasses))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0.2, 0, 0.01, 0), "npc"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
if(!is.null(featureValues))
{
if(is.factor(featureValues))
{
featureValuesData <- data.frame(Group = featureValues)
featureValuesPlot <- ggplot2::ggplot(featureValuesData, ggplot2::aes(1:length(featureValues), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(name = featureName, values = groupColours) + ggplot2::geom_tile(ggplot2::aes(fill = Group)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 0, 0), "npc"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
} else # Numeric data about the samples.
{
featureValuesData <- data.frame(Class = knownClasses, measurements = featureValues)
featureValuesPlot <- ggplot2::ggplot(featureValuesData, environment = environment()) +
ggplot2::geom_point(ggplot2::aes(x = 1:length(featureValues), y = measurements, colour = Class)) +
ggplot2::scale_colour_manual(values = classColours) +
ggplot2::scale_x_continuous(breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_continuous(breaks = c(min(featureValues), max(featureValues))) +
ggplot2::labs(x = featureName, y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 1, 0), "lines"),
axis.text = ggplot2::element_text(colour = "black"),
axis.title.x = ggplot2::element_text(size = fontSizes[4]),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize, panel.background = ggplot2::element_blank(),
panel.border = ggplot2::element_rect(colour = "black", fill = "transparent")
)
}
}
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(values = metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 1, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
classGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(classesPlot))
metricGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
if(!is.null(featureValues))
featureValuesGrob <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(featureValuesPlot))
if(!is.null(featureValues))
commonWidth <- grid::unit.pmax(classGrob[["widths"]], metricGrob[["widths"]], featureValuesGrob[["widths"]])
else
commonWidth <- grid::unit.pmax(classGrob[["widths"]], metricGrob[["widths"]])
classGrob[["widths"]] <- commonWidth
metricGrob[["widths"]] <- commonWidth
if(!is.null(featureValues))
featureValuesGrob[["widths"]] <- commonWidth
if(originalLegends == TRUE)
{
showLegends <- TRUE
metricColours <- originalmetricColours
classesPlot <- ggplot2::ggplot(classData, ggplot2::aes(1:length(knownClasses), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(values = classColours) + ggplot2::geom_tile(ggplot2::aes(fill = Class)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(knownClasses))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0.2, 0, 0.01, 0), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
classGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(classesPlot))
if(!is.null(featureValues) && is.factor(featureValues))
{
featureValuesPlot <- ggplot2::ggplot(featureValuesData, ggplot2::aes(1:length(featureValues), factor(1)), environment = environment()) +
ggplot2::scale_fill_manual(name = featureName, values = groupColours) + ggplot2::geom_tile(ggplot2::aes(fill = Group)) +
ggplot2::scale_x_continuous(expand = c(0, 0), breaks = NULL, limits = c(1, length(featureValues))) +
ggplot2::scale_y_discrete(expand = c(0, 0), breaks = NULL) +
ggplot2::labs(x = '', y = '') + ggplot2::theme(plot.margin = grid::unit(c(0, 0, 0, 0), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize)
featureValuesGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(featureValuesPlot))
} else {featureValuesGrobUnused <- grid::grob()}
plotData[, "Metric"] <- unlist(metricValues)
classLegend <- NULL
if(is.list(metricColours))
classLegend <- paste(levels(knownClasses)[1], NULL)
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(name = paste(classLegend, metricText, sep = ''),
values = if(is.list(metricColours)) metricColours[[1]] else metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 0, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
metricGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
if(!is.null(featureValues) && is.factor(featureValues))
commonWidth <- grid::unit.pmax(classGrobUnused[["widths"]], metricGrobUnused[["widths"]], featureValuesGrobUnused[["widths"]])
else
commonWidth <- grid::unit.pmax(classGrobUnused[["widths"]], metricGrobUnused[["widths"]])
metricGrobUnused[["widths"]] <- commonWidth
classGrobUnused[["widths"]] <- commonWidth
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesGrobUnused[["widths"]] <- commonWidth
classLegend <- classGrobUnused[["grobs"]][[which(sapply(classGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesLegend <- featureValuesGrobUnused[["grobs"]][[which(sapply(featureValuesGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
else
featureValuesLegend <- grid::grob()
if(showLegends == TRUE)
firstLegend <- metricGrobUnused[["grobs"]][[which(sapply(metricGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
metricPlot <- ggplot2::ggplot(plotData, ggplot2::aes(name, type)) + ggplot2::geom_tile(ggplot2::aes(fill = Metric)) +
ggplot2::scale_fill_manual(name = paste(levels(knownClasses)[2], metricText),
values = if(is.list(metricColours)) metricColours[[2]] else metricColours, na.value = "grey", drop = FALSE) + ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::scale_y_discrete(expand = c(0, 0)) + ggplot2::theme_bw() +
ggplot2::theme(axis.ticks = ggplot2::element_blank(),
axis.text.x = if(showXtickLabels == TRUE) ggplot2::element_text(angle = 45, hjust = 1, size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.text.y = if(showYtickLabels == TRUE) ggplot2::element_text(size = fontSizes[3], colour = "black") else ggplot2::element_blank(),
axis.title.x = ggplot2::element_text(size = fontSizes[2]),
axis.title.y = ggplot2::element_text(size = fontSizes[2]),
plot.margin = grid::unit(c(0, 1, 1, 1), "lines"),
legend.title = ggplot2::element_text(size = fontSizes[4]),
legend.text = ggplot2::element_text(size = fontSizes[5]),
legend.position = ifelse(showLegends, "right", "none"),
legend.key.size = legendSize) + ggplot2::labs(x = xAxisLabel, y = yAxisLabel)
metricGrobUnused <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(metricPlot))
metricGrobUnused[["widths"]] <- commonWidth
secondLegend <- metricGrobUnused[["grobs"]][[which(sapply(metricGrobUnused[["grobs"]], function(grob) grob[["name"]]) == "guide-box")]]
}
if(showLegends == TRUE)
{
classesHeight <- grid::unit(1 / (mapHeight + 1), "npc")
if(!is.null(featureValues) && is.factor(featureValues))
legendWidth <- max(sum(classLegend[["widths"]]), sum(firstLegend[["widths"]]), sum(featureValuesLegend[["widths"]]))
else
legendWidth <- max(sum(classLegend[["widths"]]), sum(firstLegend[["widths"]]))
featureValuesHeight <- grid::unit(0, "cm")
if(!is.null(featureValues))
{
if(is.factor(featureValues))
featureValuesHeight <- featureValuesLegend[["heights"]][3]
else
featureValuesHeight <- classesHeight
}
if(is.list(metricColours))
legendHeight <- (grid::unit(1, "npc") - featureValuesHeight) * (mapHeight / (mapHeight + 1) / 2)
else
legendHeight <- (grid::unit(1, "npc") - featureValuesHeight) * (mapHeight / (mapHeight + 1))
widths <- grid::unit.c(unit(1, "npc") - legendWidth, legendWidth)
heights <- grid::unit.c(unit(1 / (mapHeight + 1), "npc"), featureValuesHeight, legendHeight)
if(is.list(metricColours))
{
heights <- grid::unit.c(heights, legendHeight)
} else # Greyscale legend.
{
heights <- grid::unit.c(heights, unit(1, "npc") - legendHeight - featureValuesHeight - grid::unit(1 / (mapHeight + 1), "npc"))
}
}
else
{
widths <- grid::unit(1, "npc")
heights <- grid::unit.c(grid::unit(1 / (mapHeight + 1), "npc"), featureValuesHeight, grid::unit(1, "npc") - featureValuesHeight - grid::unit(1 / (mapHeight + 1), "npc"))
}
classLegend[["vp"]][["valid.just"]] <- c(0.7, 0.5)
if(!is.null(featureValues) && is.factor(featureValues))
featureValuesLegend[["vp"]][["valid.just"]] <- c(0.7, 0.33)
grobTable <- gtable::gtable(widths, heights)
grobTable <- gtable::gtable_add_grob(grobTable, classGrob, 1, 1)
if(!is.null(featureValues))
grobTable <- gtable::gtable_add_grob(grobTable, featureValuesGrob, 2, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, grid::grob(), 2, 1)
if(showLegends == TRUE)
{
if(is.list(metricColours))
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1, 4, 1)
else
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1, 3, 1)
} else
{
grobTable <- gtable::gtable_add_grob(grobTable, metricGrob, 3, 1)
}
if(showLegends == TRUE)
{
grobTable <- gtable::gtable_add_grob(grobTable, classLegend, 1, 2)
grobTable <- gtable::gtable_add_grob(grobTable, featureValuesLegend, 2, 2)
}
if(showLegends == TRUE && !is.list(metricColours))
{
firstLegend[["vp"]][["valid.just"]] <- c(0.62, 0.5)
grobTable <- gtable::gtable_add_grob(grobTable, firstLegend, 3, 2)
}
if(showLegends == TRUE && is.list(metricColours))
{
firstLegend[["vp"]][["valid.just"]] <- c(0.62, 0.5)
secondLegend[["vp"]][["valid.just"]] <- c(0.62, 0.4)
grobTable <- gtable::gtable_add_grob(grobTable, firstLegend, 3, 2)
grobTable <- gtable::gtable_add_grob(grobTable, secondLegend, 4, 2)
}
wholePlot <- gridExtra::arrangeGrob(grobTable, top = grid::textGrob(title, vjust = 0.5, gp = grid::gpar(fontsize = fontSizes[1])))
grid::grid.draw(wholePlot)
wholePlot
})
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