Update README.md

README.md

@@ -7,16 +7,31 @@ A quick R Markdown HTML report template that will make a barplot and table with
 ./compile-report.R "/path/to/my_peaks_dir"
 ```
 
-## Example
+## Options
+- `-n`: Name of report file to output (e.g. `-n foo` outputs `foo.Rmd` and `foo.html`)
+- `--height`: Height of the boxplot
+- `--width`: Width of the boxplot
+
+__NOTE:__ Large figures may not be displayed at full size when viewing the HTML, try right-clicking and selecting View Image.
+
+## Example 
 You can try it out on the included test data:
 
 ```bash
 ./compile-report.R test/
 ```
+Output the report file as `test-report.html` with a 8x8 boxplot
+```bash
+./compile-report.R -n "test-report" --height 8 --width 8 test
+```
+
+
 
 # Software
 - R version 3.3.0+
   - `ggplot2`
   - `DT`
   - `scales`
+  - `optparse`
+  - `tools`
 - pandoc 1.13+