Added option to render to pdf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: repcred
 Type: Package
 Version: 0.0.1
-Date: 2024-02-13
+Date: 2024-02-15
 Authors@R: c(person("Susanna", "Marquez", role=c("aut", "cre"), 
                     email="[email protected]"),
                      person("AIRR Community", role=c("cph")))

R/repcred-core.R

@@ -23,15 +23,16 @@ repcredWeb <- function(appDir=system.file("shiny-app",
 #' @param downsample  Whether report will downsample repertoire
 #' @param genome_file A reference set of the V(D)J alleles.
 #' @param outdir      Directory where the report will be generated
+#' @param format Output format: html, pdf, all
 #' @return Path to the credibility report. 
 #' 
 #' @examples
 #' 
 #' rep_file <- system.file(package="repcred", "extdata", "ExampleDb.tsv")
 #' repcred_report(rep_file, tempdir())
 #' @export
-repcred_report <- function(rep, outdir=NULL,genome_file=NULL, downsample=TRUE) {
-
+repcred_report <- function(rep, outdir=NULL,genome_file=NULL, downsample=TRUE, format=c("html", "pdf", "all")) {
+    format <- match.arg(format)
     if (file.exists(rep)) {
         if (is.null(outdir)) {
             outdir <- dirname(rep)
@@ -42,7 +43,7 @@ repcred_report <- function(rep, outdir=NULL,genome_file=NULL, downsample=TRUE) {
 
     tryCatch(
         {
-            report_path <- render_report(rep, outdir,genome_file,downsample)
+            report_path <- render_report(rep, outdir,genome_file,downsample, format)
         },
         error = function(e) {
             stop(safeError(e))
@@ -96,11 +97,13 @@ getCoreStats <- function(data){
 #' 
 #' @param rep Path to repertoire 
 #' @param outdir Directory where the report will be generated
-#' @param downsample Whether report will downsample repertoire
 #' @param genome  A reference set of the V(D)J alleles.
+#' @param downsample Whether report will downsample repertoire
+#' @param format Output format: html, pdf, all
 #' @export
-render_report <- function(rep,outdir,genome=NULL,downsample) {
+render_report <- function(rep,outdir,genome=NULL,downsample=TRUE, format=c("html","pdf","all")) {
     path = "../rstudio/templates/project/project_files/"
+    format <- match.arg(format)
     if (!dir.exists(outdir)) {
         dir.create(outdir, recursive = T)
     }
@@ -112,18 +115,38 @@ render_report <- function(rep,outdir,genome=NULL,downsample) {
 
     #setwd("../rstudio/templates/project/project_files/")
 
+    if (format == "html") {
+        output_format <- 'bookdown::gitbook'
+    } else if (format == "pdf") {
+        output_format <- 'bookdown::pdf_book'
+    } else {
+        output_format <- format
+    }
+
     # render
     xfun::in_dir(
         outdir,
         book <- bookdown::render_book(
             input = ".",
-            output_format='bookdown::gitbook',
+            output_format=output_format,
             config_file ="_bookdown.yml",
             clean=FALSE,
             new_session=FALSE,
             params=list("rep"=rep, outdir=outdir,"genome_file"=genome,
                         "downsample"=downsample))
     )
+    if (format %in% c("pdf", "all")) {
+        is_pdf <- grepl("_main.pdf$",book)
+        for (i in which(is_pdf)) {
+            book_i <- gsub("_main.pdf$","repcred-report.pdf",book[i])
+            try(
+                if (file.rename(book[i],book_i)) {
+                    book[i] <- book_i
+                }
+            )
+        }
+    }
+
     book
 }
 

inst/repcred.R

@@ -8,6 +8,7 @@
 #   -r  Repertoire file, in AIRR (TSV) format.
 #   -o  Output directory. Will be created if it does not exist.
 #       Defaults to tempdir().
+#   -f  Output format: html, pdf, all
 #   -h  Display help.
 
 # Imports
@@ -19,6 +20,7 @@ suppressPackageStartupMessages(library("repcred"))
 REP <- NULL
 OUTDIR <- tempdir()
 DOWN <- TRUE
+FORMAT <- "html"
 
 # Define commmandline arguments
 opt_list <- list(make_option(c("-r", "--rep"), dest="REP", default=REP,
@@ -27,7 +29,9 @@ opt_list <- list(make_option(c("-r", "--rep"), dest="REP", default=REP,
                              help="Downsample."),
                  make_option(c("-o", "--outdir"), dest="OUTDIR", default=OUTDIR,
                              help=paste("Output directory. Will be created if it does not exist.",
-                                        "\n\t\tDefaults to the current working directory."))
+                                        "\n\t\tDefaults to the current working directory.")),
+                 make_option(c("-f", "--format"), dest="FORMAT", default=FORMAT,
+                             help="Output format: html, pdf, all")
 )
 # Parse arguments
 opt <- parse_args(OptionParser(option_list=opt_list))
@@ -43,19 +47,25 @@ if (!("REP" %in% names(opt))) {
     }
 }
 
+# Check format
+if (!(any(opt$FORMAT %in% c("html", "pdf", "all"))) | length(opt$FORMAT)>1) {
+    stop("Output format (-f/--format) must be one of: html, pdf, all")
+} 
+
 opt$OUTDIR <- normalizePath(opt$OUTDIR)
 dir.create(opt$OUTDIR, recursive = T)
 
 message("\nRunning repcred")
 message("|- Repertoire:\n", normalizePath(opt$REP))
 message("|- Downsample:\n", opt$DOWN)
-message("|- Output dir:\n", normalizePath(opt$OUTDIR),"\n")
+message("|- Output dir:\n", normalizePath(opt$OUTDIR))
+message("|- Output format:\n", opt$FORMAT,"\n")
 
 sink(file(file.path(opt$OUTDIR,"message.log"),"wt"), type="message")
 sink(file(file.path(opt$OUTDIR,"output.log"),"wt"), type="output")
 
 tryCatch(
-    report <- render_report(rep=opt$REP, outdir=opt$OUTDIR, downsample = opt$DOWN),
+    report <- render_report(rep=opt$REP, outdir=opt$OUTDIR, downsample = opt$DOWN, format=opt$FORMAT),
     error = function(e) {
         stop(safeError(e))
     }

inst/rstudio/templates/project/project_files/index.Rmd

@@ -21,6 +21,11 @@ output:
          download: yes
          sharing: no
          keep_md: true
+    bookdown::pdf_book:
+        keep_tex: false
+        toc: true
+        base_format: rmarkdown::pdf_document
+        number_sections: true         
 params:
    date: !r date()
    echo:  FALSE