#' Does a rough, first pass SNP FISH analysis for a given directory
#'
#' @param masterdir directory to search for all sub yaml-files for standard
#' analysis
#' @param outdir directory in which to output SNP plots
#' @param SNPTableFlag Will produce plots on SNP tables if they exist. Default
#' is false.
AnalyzeSNPDirectory <-
function(masterdir, outdir, SNPTableFlag = FALSE) {
yaml.groups <- GetAllYamlGroupsinDir(masterdir)
for (i in 1:length(yaml.groups)) {
data.Files <-
ExtractFilesFromYamlGroup(yaml.groups[[i]], masterdir)
exp.data <- data.Files[[1]]
guide.table <- data.Files[[2]]
MakeGuideTablePlots(exp.data, guide.table, outdir)
if (SNPTableFlag) {
tmr.table <- data.Files[[3]]
cy.table <- data.Files[[4]]
SNPDir <- paste(outdir, "/SNPChannelData", sep = "")
if (!dir.exists(SNPDir)) {
dir.create(SNPDir)
}
MakeStackedCellCountPlot(exp.data, tmr.table, SNPDir)
MakeTotalCellCountPie(exp.data, tmr.table, SNPDir)
MakeStackedCellCountPlot(exp.data, cy.table, SNPDir)
MakeTotalCellCountPie(exp.data, cy.table, SNPDir)
}
}
}
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