#' Show Usage of \code{virustiter} Package
#'
#' Display succinct summary of functions and work flow in \code{virustiter}.
#'
#' @return
#'
#' No value returned, a window is opened with helpful information.
#'
#' @export
#'
usage <- function() {
txt <- c(
" Workflow:",
" img <- getImages() # read paired images with EBImage",
" df <- parseImages(img) # extract nuclear information and target mfi",
"",
" pd <- data.frame(file = levels(df$file), moi = moi, unit = unit)",
" Or for a single plate organized by well:",
" pd <- data.frame(well.info(unique(df$well)), moi = moi, unit = unit)",
" Or if multiple plates are used:",
" pd <- data.frame(well.info(unique(df$labels)), moi = moi, unit = unit)",
"",
" df <- mergePdata(pd, df) # merge with phenotype data in 'pd'",
" bg <- getBgnd(df) # determine background by control (or well, row, or column)",
" df <- score(df, bg) # assign positive values from background",
" res <- tally(df) # tally positives and negatives and return data.frame",
" fm <- getFit(res) # get model fit(s) from either res or scored data frame",
" cf <- getTiter(fm) # get titer infectious units per ml +/- 95% CI",
"",
" Support:",
" checkImages(path) # check (and display) paired images",
" list.images(path) # list image files in the given path",
" getZero(x) # find most common non-zero pixel in each image frame",
" setZero(x) # rescale each image frame to the most common zero value",
" nucMask(dapi) # extract nuclear mask from dapi image(s) or file(s)",
" trimMask(mask) # remove objects based on size from mask",
" cellMask(mask) # expand a nuclear mask into a cell mask",
" edgeObjects(mask) # identify objects near the edge of a mask",
" findObjects(expr, df) # find objects in data.frame identified by expr",
" getVal(mask, ref) # extract one 'computeFeatures' value using mask and ref",
" p2p() # interactively measure point-to-point distances",
" plotHist(df) # histogram of each well with background values",
" plotDens(df) # densityplot of each well with background values",
" plotPlate(df) # plot plate showing positives",
" plotWell(df, well) # plot each cell in a well showing positives and sizes",
" plotFit(fm) # plot fit(s) with calculated values using base graphics",
" addOneFit(fm) # add best-fit line to existing base graph",
" getAIC(df, bg) # create and evaluate fitted model(s) from df at bg values",
" getTiter(fm) # get titer as IU per ml (if volume units were used)",
" getEC63(fm) # get volume required for 1 infectious units +/- 95% CI",
" getShift(mask, tgt) # get optimal x-y shift to align tgt with (nuc) mask",
" translate(x, v) # apply (optimal) x-y shift in v to image x",
"")
ft <- tempfile()
writeLines(txt, con = ft, sep = "\n")
file.show(ft, title = "Information on 'virustiter' package")
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.