exportPlots: Plot the algorithms results with ggplot2

In bgbrink/ddPCRclust: Clustering algorithm for ddPCR data

Description

A convinience function that takes the results of the ddPCRclust algorithm, plots them using the ggplot2 library and a custom colour palette and saves the plots to a folder.

Usage

exportPlots(data, directory, annotations, format = "png", invert = FALSE)

Arguments

data	The result of the ddPCRclust algorithm
directory	The parent directory where the files should saved. A new folder with the experiment name will be created (see below).
annotations	Some basic metadata about the ddPCR reaction. If you provided ddPCRclust a template, this paramater can be filled with the corresponding field in the result. Otherwise, you have to provide a character vector containing a name and the the color channels, e.g. c(Name='ddPCR_01-04-2017', Ch1='HEX', Ch2='FAM')
format	Which file format to use. Can be either be a device function (e.g. png), or one of 'eps', 'ps', 'tex' (pictex), 'pdf', 'jpeg', 'tiff', 'png', 'bmp', 'svg' or 'wmf' (windows only). See also ggsave
invert	Invert the axis, e.g. x = Ch2.Amplitude, y = Ch1.Amplitude

Value

None

Examples

# Read files
exampleFiles <- list.files(paste0(find.package('ddPCRclust'), '/extdata'), full.names = TRUE)
files <- readFiles(exampleFiles[3])
# To read all example files uncomment the following line
# files <- readFiles(exampleFiles[1:8])

# Read template
template <- readTemplate(exampleFiles[9])

# Run ddPCRclust
result <- ddPCRclust(files, template)

# Export the plots
dir.create('./Results')
exportPlots(data = result, directory = './Results/', annotations = result$annotations)

bgbrink/ddPCRclust documentation built on Nov. 10, 2019, 7:10 a.m.