a4 (version 1.20.0)

probabilitiesPlot: Function to plot the probabilities to belong to a certain class in binary classification problems.

Description

Function to plot the probabilities to belong to a certain class in binary classification problems. These probabilities are often calculated using a logistic regression model. The class membership of the samples is displayed using a colored strip (with legend below the plot).

Usage

probabilitiesPlot(proportions, classVar, sampleNames, plot = TRUE, barPlot = FALSE, layout = TRUE, main = NULL, sub = NULL, ...)

Arguments

proportions

A vector containing the calculated probabilities to belong to a certain class in binary classification problems. These probabilities are often calculated using a logistic regression model.

classVar

A vector containing the class where the sample belongs to

sampleNames

A vector with the names of the samples

plot

logical. If FALSE, nothing is plotted.

barPlot

Should a barplot be drawn (TRUE) or a scatterplot like MCREstimate-type scores plot (the default, FALSE).

layout

boolean indicating whether mcrPlot should prespecify a layout for a single plot (default, TRUE) or whether the user takes care of the layout (FALSE)

main

Main title for the scores plot; if not supplied, 'Scores Plot' is used as a default

sub

Subtitle for the scores plot; if not supplied, the classification technique and the chosen number of features are displayed

...

Additional graphical parameters to pass to the plot function

See Also

logReg

Examples

if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)
  ALL$BTtype <- as.factor(substr(ALL$BT,0,1))

  logRegRes <- logReg(geneSymbol = "HLA-DPB1", object = ALL, groups = "BTtype")

  # scoresplot
  probabilitiesPlot(proportions = logRegRes$fit, classVar = logRegRes$y,
    sampleNames = rownames(logRegRes), main = 'Probability of being a T-cell type ALL')
  # barplot
  probabilitiesPlot(proportions = logRegRes$fit, classVar = logRegRes$y, barPlot=TRUE,
    sampleNames = rownames(logRegRes), main = 'Probability of being a T-cell type ALL')
}