plotElasticNet: Plot elastic net results
In CBIIT/rcellminerElasticNet: rcellminerElasticNet

Description Usage Arguments Details Value Note Author(s) References Examples

Creates a plot for elastic net results similar to the GDSC plots (http://www.cancerrxgene.org/help/)

plotElasticNet(
  drugName,
  weights,
  drugAct,
  molDb,
  numCellLines,
  numFeatures = 10,
  featureAnnotations = NULL,
  showCellLineLabels = TRUE,
  pdfFilename = NULL,
  thresholdValues = FALSE,
  isMutBin = TRUE,
  axisScaling = NULL,
  topMarWt = 4,
  bottomMarWt = 2.75,
  leftMarHeatmap = 5,
  pdfWidth = 10,
  responseLabel = "Drug Activity",
  verbose = TRUE
)

`drugName`	a string with the name of drug
`weights`	a named vector of values with the elastic net weights for a set of features
`drugAct`	a matrix of drug activity values, a value for each drug tested for each cell line
`molDb`	a list of matrix of supported data types. The list must use the following prefixes: exp: gene expression, mir: miRNA, mut: mutations, pro: protein, mda: metadata, cop: copy number variations
`numCellLines`	an integer of the number of cell lines to be plotted. This function will take the top (by drug activity) numCellLines/2 and the bottom numCellLines/2 for plotting
`numFeatures`	an integer of the number of features to be plotted; default 10
`featureAnnotations`	a vector of optional annotations that will be appended to feature names in parentheses
`showCellLineLabels`	a boolean whether to show cell line labels; default TRUE
`pdfFilename`	a string filename for saving the image to a PDF
`thresholdValues`	a boolean to threshold values to an upper limit of 3 and a lower bound of -3
`isMutBin`	a boolean whether the mutation values are binarized (default: TRUE)
`axisScaling`	a scaling factor for the the feature labels, if not use a default will be used depending on if the there annotations
`topMarWt`	a user selected top margin for the the feature weights (default: 4)
`bottomMarWt`	a user selected top margin for the the feature weights (default: 2.75)
`leftMarHeatmap`	the left margin for the the heatmap and drug activity; can be increased to handle longer labels (default: 5)
`pdfWidth`	the width of the PDF (default: 10)
`responseLabel`	a string describing the response vector (default: "Drug Activity")
`verbose`	a boolean, whether to display debugging information

This function uses layout() and may conflict if embedded in other plots using layout(). If the pdfFilename argument is used then the image will not be displayed on the screen.

if verbose is TRUE then a list with the plotted drug activity values, heatmap values, and cell line order will be returned

plotElasticNet does not return values; a plot is produced

Make sure the numFeatures is less than the length of the weights

Augustin Luna

GDSC Website: http://www.cancerrxgene.org/help/