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

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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

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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

Author(s)

Willem Talloen and Tobias Verbeke

See Also

logReg

Examples

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## Not run: 
  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')
}

## End(Not run)

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