plotElasticNet: Plot elastic net results

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

View source: R/plotElasticNet.R

Description

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

Usage

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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
)

Arguments

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

Details

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.

Value

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

Note

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

Author(s)

Augustin Luna

References

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

Examples

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#plotElasticNet("PD-0325901", weights, binMutCCLE, drugActCCLE, genExpCCLE, 400, 10)

CBIIT/rcellminerElasticNet documentation built on Sept. 8, 2020, 6:21 p.m.