densityFun: Create an image with a density curve of the intensities

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Create an image with a density curve of the intensities

Description

This function (from functions_imagesQC.R) creates an image with a density curve of the intensities for all arrays in the raw or normalized dataset (depending on the object passed).

Usage

densityFun(
  Data,
  plotColors = NULL,
  normMeth = "",
  WIDTH = 1000,
  HEIGHT = 1414,
  POINTSIZE = 24,
  MAXARRAY = 41
)

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch)
plotColors	(Status: required, Default:NULL) Vector of colors assigned to each array. (datatype: character)
normMeth	(Status: required when Data is a normalized data object, Default:"") String indicating the normalization method used (see normalizeData function for more information on the possible values). (datatype: character)
WIDTH	(Status: optional, Default:1000) png image width (datatype: number)
HEIGHT	(Status: optional, Default:1414) png image height (datatype: number)
POINTSIZE	(Status: optional, Default:24) png image point size (datatype: number)
MAXARRAY	(Status: optional, Default:41) threshold to adapt the image to the number of arrays (datatype: number)

Value

A PNG image of the raw or normalized density plots of the arrays, called "DensityHistogram"

Examples

# By default, before the normalization the script will call:
# densityFun(Data=rawData, plotColors)
# and after normalization:
# densityFun(Data=normData, plotColors, normMeth=normMeth)

ammar257ammar/ArrayAnalysis-Bioconductor documentation built on Jan. 29, 2024, 7:21 a.m.