performancePlot: Plot Performance Measures for Various Classifications

In ClassifyR: A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Description

Draws a graphical summary of a particular performance measure for a list of classifications

Usage

  ## S4 method for signature 'list'
performancePlot(results, aggregate = character(),
                    xVariable = c("classificationName", "datasetName", "selectionName",
                              "validation"),
                performanceName = NULL,
                    boxFillColouring = c("classificationName", "datasetName", "selectionName",
                                     "validation", "None"),
                boxFillColours = NULL,
                    boxLineColouring = c("classificationName", "datasetName", "selectionName",
                                     "validation", "None"),
                boxLineColours = NULL,
                    rowVariable = c("None", "validation", "datasetName", "classificationName",
                                 "selectionName"),
                    columnVariable = c("datasetName", "classificationName", "validation",
                                   "selectionName", "None"),
                 yLimits = c(0, 1), fontSizes = c(24, 16, 12, 12), title = NULL,
                xLabel = "Analysis", yLabel = performanceName,
                margin = grid::unit(c(0, 0, 0, 0), "lines"), rotate90 = FALSE,
                showLegend = TRUE, plot = TRUE)

Arguments

results	A list of ClassifyResult objects.
aggregate	A character vector of the levels of xVariable to aggregate to a single number by taking the mean. This is particularly meaningful when the cross-validation is leave-k-out, when k is small.
xVariable	The factor to make separate boxes for.
performanceName	The name of the performance measure to make comparisons of. This is one of the names printed in the Performance Measures field when a ClassifyResult object is printed.
boxFillColouring	A factor to colour the boxes by.
boxFillColours	A vector of colours, one for each level of boxFillColouring.
boxLineColouring	A factor to colour the box lines by.
boxLineColours	A vector of colours, one for each level of boxLineColouring.
rowVariable	The slot name that different levels of are plotted as separate rows of boxplots.
columnVariable	The slot name that different levels of are plotted as separate columns of boxplots.
yLimits	The minimum and maximum value of the performance metric to plot.
fontSizes	A vector of length 4. 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 font size of the titles of grouped plots, if any are produced. In other words, when rowVariable or columnVariable are not NULL.
title	An overall title for the plot.
xLabel	Label to be used for the x-axis.
yLabel	Label to be used for the y-axis of overlap percentages.
margin	The margin to have around the plot.
rotate90	Logical. IF TRUE, the plot is horizontal.
showLegend	If TRUE, a legend is plotted next to the plot. If FALSE, it is hidden.
plot	Logical. IF TRUE, a plot is produced on the current graphics device.

Details

Possible values for slot names are "datasetName", "classificationName", and "validation". If "None", then that graphic element is not used.

If there are multiple values for a performance measure in a single result object, it is plotted as a boxplot, unless aggregate is TRUE, in which case the all predictions in a single result object are considered simultaneously, so that only one performance number is calculated, and a barchart is plotted.

Value

An object of class ggplot and a plot on the current graphics device, if plot is TRUE.

Author(s)

Dario Strbenac

Examples

  predicted <- list(data.frame(sample = sample(LETTERS[1:10], 20, replace = TRUE),
                               class = factor(rep(c("Healthy", "Cancer"), each = 10))),
                    data.frame(sample = sample(LETTERS[1:10], 20, replace = TRUE),
                               class = factor(rep(c("Healthy", "Cancer"), each = 10))),
                    data.frame(sample = sample(LETTERS[1:10], 20, replace = TRUE),
                               class = factor(rep(c("Healthy", "Cancer"), each = 10))),
                    data.frame(sample = sample(LETTERS[1:10], 20, replace = TRUE),
                               class = factor(rep(c("Healthy", "Cancer"), each = 10))))
  actual <- factor(rep(c("Healthy", "Cancer"), each = 5))
  result1 <- ClassifyResult("Example", "Differential Expression", "t-test",
                            LETTERS[1:10], LETTERS[10:1], 100, list(1:100, c(1:9, 11:101)),
                            list(c(1:3), c(2, 5, 6), c(1:4), c(5:8), 1:5),
                            list(function(oracle){}), predicted, actual,
                            validation = list("permuteFold", 2, 2))
  result1 <- calcCVperformance(result1, "macro F1")

  predicted <- list(data.frame(sample = sample(LETTERS[1:10], 20, replace = TRUE),
                               class = factor(rep(c("Healthy", "Cancer"), each = 10))),
                    data.frame(sample = sample(LETTERS[1:10], 20, replace = TRUE),
                               class = factor(rep(c("Healthy", "Cancer"), each = 10))),
                    data.frame(sample = sample(LETTERS[1:10], 20, replace = TRUE),
                               class = factor(rep(c("Healthy", "Cancer"), each = 10))),
                    data.frame(sample = sample(LETTERS[1:10], 20, replace = TRUE),
                               class = factor(rep(c("Healthy", "Cancer"), each = 10))))
  result2 <- ClassifyResult("Example", "Differential Variability", "Bartlett Test",
                            LETTERS[1:10], LETTERS[10:1], 100, list(1:100, c(1:5, 11:105)),
                            list(c(1:3), c(4:6), c(1, 6, 7, 9), c(5:8), c(1, 5, 10)),
                            list(function(oracle){}), predicted, actual,
                            validation = list("permuteFold", 2, 2))
  result2 <- calcCVperformance(result2, "macro F1")
  
  performancePlot(list(result1, result2), performanceName = "Macro F1 Score",
                  title = "Comparison", boxLineColouring = "None", columnVariable = "None")

ClassifyR documentation built on Nov. 8, 2020, 6:53 p.m.