Basic Rmd report structure

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CancerEvolutionVisualization
 Title: Publication Quality Phylogenetic Tree Plots
-Version: 1.1.1
-Date: 2022-11-18
+Version: 1.1.0
+Date: 2023-02-15
 Authors@R: c(
 	person("Paul Boutros", role = "cre", email = "PBoutros@mednet.ucla.edu"),
 	person("Adriana Salcedo", role = "aut"),
@@ -19,7 +19,8 @@ Imports:
     plyr,
     grDevices,
     utils,
-    stringr
+    stringr,
+    rmarkdown
 Suggests:
     testthat,
 	knitr

NEWS

@@ -1,6 +1,7 @@
-CancerEvolutionVisualization 1.1.1 2022-11-18 (Helena Winata)
+CancerEvolutionVisualization 1.1.0 2023-02-15 (Dan Knight, Helena Winata)
 
 ADDED
+* CEV report template and public function
 * Generic functions to generate accompanying heatmaps
 
 

R/CEV.report.R

@@ -0,0 +1,18 @@
+CEV.report <- function(
+    output.filename,
+    title,
+    author,
+    date = NULL
+    ) {
+    report.params <- list(
+        title = title,
+        author = author,
+        date = if (!is.null(date)) date else Sys.Date()
+        );
+
+    rmarkdown::render(
+        'inst/test.Rmd',
+        output_file = output.filename,
+        params = report.params
+        );
+    }

inst/CEV.report.Rmd

@@ -0,0 +1,16 @@
+---
+params:
+    title:
+    author:
+    date:
+title: '`r params$title`'
+author: '`r params$author`'
+date: '`r params$date`'
+output: pdf_document
+---
+
+# Tree
+
+# Mutation Assignment Heatmap
+
+# Clone Summary Heatmap