added functions to export plot and index figures in rna-seq_analysis

scripts/RSnakeChunks/R/export_plot.R

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+#' @title Export the current device to one or several files with user-specified format(s).
+#' @author Jacques van Helden
+#' formats.
+#' @examples
+#' ExportPLot(file.prefix = "test",
+#'    export.formats = c("postscript","jpg","png","bmp","pdf"))
+#' @param  file.prefix="PlotExport"
+#' @param export.formats="pdf" # supported: postscript, jpg, png, bmp, pdf
+#' @param width=11 Width of output file (in inches)
+#' @param height=8 Height of output file (in inches)
+#' @param horizontal=TRUE parameter passed to postscript()
+#' @param dpi=72 dots per inch. Automatically converted to width and height in pixels for bitmap formats. 
+#' @param verbose = 0 level of verbosity
+#' @param ... Additional parameters are passed to the export method
+#' @export             
+ExportPLot <- function(file.prefix = "PlotExport",
+                        export.formats = "pdf", # supported: postscript, jpg, png, bmp, pdf
+                        width = dev.size(units = "in")[1], # in inches
+                        height = dev.size(units = "in")[1], # in inches
+                        horizontal = TRUE,
+                        dpi = 72,
+                        verbose = 0, 
+                        ... ## Additional parameters are passed to the export method
+) {
+
+  f <- export.formats[1]
+  for (f in export.formats) {
+    source.dev <- dev.cur();
+    new.dev <- OpenPlotDevice(file.prefix, fig.format = f, width = width,height = height,horizontal = horizontal, dpi = dpi, verbose, ...)
+#    new.dev <- dev.cur()
+    dev.set(which = source.dev)
+    dev.copy(which = new.dev)
+    dev.set(which = new.dev)
+    dev.off()
+    dev.set(which = source.dev) ## This is required because dev.off() returns to the first, not the last, device
+  }
+}
+
+#' @title open plot device with parameters adapted to the specificities of the different device functions. 
+#' @author Jacques van Helden
+#' @param file.prefix file prefix (the extension will be concatenated according to format)
+#' @param fig.format="pdf" file firmat. Supported: postscript, jpg, png, bmp, pdf
+#' @param width=8 Width of output file (in inches).
+#' @param height=8 Height of output file (in inches)
+#' @param horizontal=TRUE parameter passed to postscript()
+#' @param dpi=72 dots per inch. Automatically converted to width and height in pixels for bitmap formats. 
+#' @param verbose = 0 level of verbosity
+#' @return returns the new device
+#' @export
+OpenPlotDevice <- function(file.prefix,
+                             fig.format = 'pdf',
+                             width = 8,
+                             height = 8,
+                             horizontal = TRUE,
+                             dpi = 72, ## Points per Inch (screen resolution by default)
+                             verbose = 0,
+                             ...) {  
+
+  fig.format <- tolower(fig.format)  
+  file.ext <- c(
+    x11 = "x11",
+    postscript = "ps",
+    pdf = "pdf",
+    ps = "ps",
+    eps = "eps",
+    jpeg = "jpg",
+    jpg = "jpg",
+    bmp = "bmp",
+    png = "png")
+  file.name <- paste(file.prefix, file.ext[fig.format], sep = ".")
+  if (verbose >= 0) { message("\t\tExporting plot to file ",file.name, " ", fig.format, " format", sep = "") }
+  if ((fig.format   ==   "postscript") || (fig.format   ==   "ps")) {
+    postscript(file.name,paper = "special",width = width,height = height,horizontal = horizontal, ...)
+  } else if (fig.format   ==   "eps") {
+    postscript(file.name,paper = "special",width = width,height = height,horizontal = horizontal,onefile = F, ...)
+  } else if (fig.format   ==   "pdf") {
+    pdf(file.name, paper = "special",width = width,height = height, ...)
+  } else if ((fig.format   ==   "jpg") || (fig.format  ==  "jpeg")) {
+    jpeg(file.name,width = width * dpi, height = height * dpi, quality = 100, ...)
+  } else if (fig.format  ==  "png") {
+    png(file.name,width = width * dpi, height = height * dpi, ...)
+  } else if (fig.format  ==  "bmp") {
+    bitmap(file.name,width = width*dpi,height = height*dpi, ...)
+  } else if (fig.format  ==  "x11") {
+    x11(width = width,height = height)
+  } else {
+    stop("OpenPlotDevice()\tInvalid format: ", fig.format, ". Supported: ps, eps, pdf, jpg, png, bmp, x11")
+    return()
+  }
+  new.dev <- dev.cur()
+  return(new.dev)
+}

scripts/RSnakeChunks/R/index_figure.R

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+#' @title generate a figure chunk of R code to insert in an Rmd report
+#' @author Jacques van Helden
+#' @param name name of the chunk
+#' @param file file continaing the figure
+#' @param index.text=NULL if spcified, the chunk will be appended to it
+#' @param chunk_opt=", eval=TRUE" a string specifying one or more options to append to the chunk declaration line. Must start with a comma. 
+#' @export
+index.figure <- function(name, file, index.text = NULL, chunk.opt = ", eval=TRUE") {
+  fig.chunk <-  paste(sep = "",
+                      "
+```{r fig='", name, "' ", chunk.opt, " }
+knitr::include_graphics(path = '", file, "', auto_pdf = TRUE)
+```
+                     ")
+  if (is.null(index.text)) {
+    return(fig.chunk)
+  } else {
+    return(append(index.text, fig.chunk))
+  }
+}