#' View HumanLiver data in the scClustViz Shiny app
#'
#' A wrapper function to view the \code{HumanLiver} dataset in the
#' \code{scClustViz} Shiny app.
#'
#' @param outPath Default = "./" (the working directory). Specify the directory
#' used to save/load any analysis files you generate while exploring the
#' \code{HumanLiver} data.
#' @param imageFileType Default="pdf". The file format for saved figures. One of
#' \code{"pdf"} (generated with \code{\link[grDevices]{cairo_pdf}}),
#' \code{"eps"} (generated with \code{\link[grDevices]{cairo_ps}}),
#' \code{"tiff"} (generated with \code{\link[grDevices]{tiff}}), or
#' \code{"png"} (generated with \code{\link[grDevices]{png}}).
#' @param ... Named options that should be passed to the
#' \code{\link[shiny]{runApp}} call (these can be any of the following:
#' "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode").
#'
#' @return The function causes the scClustViz Shiny GUI app to open in a
#' seperate window.
#'
#' @examples
#' viewHumanLiver()
#'
#' @seealso \url{https://baderlab.github.io/scClustViz} for information on
#' \code{scClustViz}.
#'
#' @export
viewHumanLiver <- function(outPath="./",imageFileType="pdf",...) {
filePath <- system.file("liver/HumanLiver.RData",package="HumanLiver")
cellMarkers <- list("Hepatocytes"=c("ALB","HAMP","ARG1","PCK1","AFP","BCHE"),
"LSECs"=c("CALCRL","CD32B","VWF"),
"Cholangiocytes"=c("KRT19","EPCAM","FXDY2","CLDN4","CLDN10",
"SOX9","MMP7","CXCL1","CFTR","TFF2","KRT7","CD24"),
"Hepatic Stellate Cells"=c("ACTA2","COL1A1","TAGLN","COL1A2",
"COL3A1","SPARC","RBP1","DCN","MYL9"),
"Macrophages"=c("CD68","MARCO"),
"ab T cells"=c("CD2","CD3D","TRAC","IL32","CD3E"),
"gd T cells"=c("NKG7","FCGR3A","HOPX","GNLY"),
"NK cells"=c("GZMK","KLRF1","CCL3","CMC1"),
"Plasma cells"=c("CD27","IGHG1"),
"Mature B cells"=c("MS4A1","LTB","CD52","IGHD"),
"Erythroid cells"=c("HBB","SLC25A37","CA1","ALAS2"))
if (require("org.Hs.eg.db",quietly=T)) {
annotationDB <- org.Hs.eg.db
scClustViz::runShiny(filePath=filePath,
outPath=outPath,
cellMarkers=cellMarkers,
annotationDB=annotationDB,
rownameKeytype="SYMBOL",
imageFileType=imageFileType,
...)
} else {
scClustViz::runShiny(filePath=filePath,
outPath=outPath,
cellMarkers=cellMarkers,
imageFileType=imageFileType,
...)
}
}
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