writeBackgroundImages {blima} | R Documentation

## 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

### Author(s)

Vojtěch Kulvait

### 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 BiocManager::install('blimaTestingData').");
    }

[Package blima version 1.22.0 Index]