add report name option and example

NYU-BFX · Jul 31, 2017 · b462646 · b462646
1 parent 9dbd406
commit b462646
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/compile-report.R b/compile-report.R
@@ -1,6 +1,7 @@
 #!/usr/bin/env Rscript
 
 ## USAGE: compile_RMD_report.R report.Rmd
+## EXAMPLE: ./compile-report.R -n "peaks.by_sample.macs_broad" --height 42 --width 12 results/peaks.by_sample.macs_broad
 ## Requires pandoc version 1.13+
 # module load pandoc/1.13.1
 
@@ -15,7 +16,7 @@ library("tools")
 
 # ~~~~~ GET SCRIPT ARGS ~~~~~~~ #
 option_list <- list(
-    make_option(c("-n", "--name"), type="character", default=FALSE,
+    make_option(c("-n", "--name"), type="character", default='peaks-report',
                 dest="report_name", help="A different output name to use for the report file (excluding file extension)"),
     make_option(c("--height"), type="numeric", default=12,
                 dest = "plot_height", help="Height for boxplot [default %default]",
@@ -45,4 +46,5 @@ if(report_name != FALSE){
 }
 rmarkdown::render(input = Rmdfile, params = list(input_dir = input_dir, 
                                                  plot_height = plot_height, 
-                                                 plot_width = plot_width))
+                                                 plot_width = plot_width,
+                                                 report_name = report_name))
diff --git a/peaks-report.Rmd b/peaks-report.Rmd
@@ -10,6 +10,7 @@ params:
    input_dir: "/path/to/peaks_dir"
    plot_height: 12
    plot_width: 10
+   report_name: "peaks_report"
 ---
 
 ```{r setup, include=FALSE}
@@ -85,12 +86,14 @@ make_peaks_barplot <- function(df){
 input_dir <- normalizePath(params$input_dir)
 plot_height <- as.numeric(params$plot_height)
 plot_width <- as.numeric(params$plot_width)
+report_name <- as.character(params$report_name)
 
 bed_df <- make_bed_df(input_dir = input_dir)
 
 peaks_barplot <- make_peaks_barplot(df = bed_df)
 
 save.image(file = "loaded_data.Rdata", compress = TRUE)
+write.table(x = bed_df, file = sprintf("%s.csv", report_name), quote = FALSE, sep = ',', row.names = FALSE, col.names = TRUE)
 ```
 
 # Input dir