writeBackgroundImages {blima} | R Documentation |
This function writes images with background distribution according to foreground before and after background subtraction.
writeBackgroundImages(b, spotsToGenerate = NULL, imageType = c("jpg", "png", "eps"), channelForeground = "GrnF", channelBackground = "GrnB", SDMultiple = 3, includePearson = FALSE, outputDir = getwd(), width = 505, height = 505)
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 |
Vojtěch Kulvait
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')."); }