boxplotFun: Create an image with intensity boxplots for all arrays

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Create an image with intensity boxplots for all arrays

Description

This function (from functions_imagesQC.R) creates an image with intensity boxplots for all arrays in the raw or normalized dataset (depending on the object passed). It calls the boxplot function applied to an AffyBatch object.

Usage

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

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch)
experimentFactor	(Status: required, Default:NULL) The factor of groups. (datatype: factor)
plotColors	(Status: required, Default:NULL) Vector of colors assigned to each array. (datatype: character)
legendColors	(Status: required, Default:NULL) Vector of colors assigned to each experimental group. (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 boxplots of the arrays, called ‘DataBoxplot’

Examples

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

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