ClassifyR (version 1.2.4)

performancePlot: Plot Performance Measures for Various Classifications

Description

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

Usage

"performancePlot"(results, aggregate = FALSE, xVariable = c("classificationName", "datasetName", "validation"), performanceName = NULL, boxFillColouring = c("classificationName", "datasetName", "validation", "None"), boxFillColours = NULL, boxLineColouring = c("classificationName", "datasetName", "validation", "None"), boxLineColours = NULL, yMax = 1, fontSizes = c(24, 16, 12), title = NULL, xLabel = "Classification", yLabel = performanceName, margin = grid::unit(c(0, 1, 1, 0), "lines"), rotate90 = FALSE, plot = TRUE)

Arguments

results

A list of ClassifyResult objects.

aggregate

If TRUE, and there are multiple values of a particular performance measure stored, such as when bootstrap resampling is done, the performance measure is summarised to a single number by considering all predictions simultaneously.

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.

yMax

The maximum value of the percentage to plot.

fontSizes

A vector of length 3. 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.

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.

plot

Logical. IF TRUE, a plot is produced on the current graphics device.

Value

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

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.

Examples

  predicted <- data.frame(sample = sample(10, 100, replace = TRUE),
                          label = rep(c("Healthy", "Cancer"), each = 50))
  actual <- factor(rep(c("Healthy", "Cancer"), each = 5))
  result1 <- ClassifyResult("Example", "Differential Expression", LETTERS[1:10], LETTERS[10:1], 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(predicted), actual, list("fold", 100, 5))
  result1 <- calcPerformance(result1, "f")
  predicted[, "label"] <- sample(predicted[, "label"])
  result2 <- ClassifyResult("Example", "Differential Variability", LETTERS[1:10], LETTERS[10:1], 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(predicted), actual, validation = list("leave", 1))
  result2 <- calcPerformance(result2, "f")                            
  performancePlot(list(result1, result2), performanceName = "Precision-Recall F measure", title = "Comparison")