blima (version 1.6.0)

writeBackgroundImages: Write Background Images

Description

This function writes images with background distribution according to foreground before and after background subtraction.

Usage

writeBackgroundImages(b, spotsToGenerate = NULL, imageType = c("jpg",  "png", "eps"), channelForeground = "GrnF", channelBackground = "GrnB",  SDMultiple = 3, includePearson = FALSE, outputDir = getwd(),  width = 505, height = 505)

Arguments

b

Single beadLevelData object.

spotsToGenerate

NULL for generate images for all spots from b. Otherwise specifies logical vector of the length equals to the number of arrays in b with TRUE for images to generate.

imageType

Type of images produced, either jpg, png or eps

channelForeground

Name of channel of foreground.

channelBackground

Name of channel of background.

SDMultiple

Correct on this level.

includePearson

Include Pearson corelation.

outputDir

Directory where to output images.

width

Width of image (default 505 fits well for 86mm 150dpi illustration in Bioinformatics journal:)

height

Height of image

Examples

if(require("blimaTestingData") && interactive())
{
    #Write background images before and after correction for background into /tmp directory. This function creates two jpg images for condition D. Output files are /tmp/6898481102_D_CORRECTED.jpg and /tmp/6898481102_D.jpg.
    data(blimatesting)
    p = pData(blimatesting[[2]]@experimentData$phenoData)
    spotsToGenerate = p$Group %in% "D";
    writeBackgroundImages(blimatesting[[2]], imageType="jpg", spotsToGenerate=spotsToGenerate, includePearson=FALSE, outputDir="/tmp", width=505, height=505)
}else
{
    print("To run this example, please install blimaTestingData package from bioconductor by running biocLite('blimaTestingData').");
}