Output chart report as a Word document only

HTML support breaks the Word output and it is not used
Partial fix for #46

NEWS.md

@@ -2,6 +2,7 @@
 **2021-06-10**
 
 - Fix a critical bug in the consolidate and summarize addin
+- Fix problems with chart generation in the analyze addin #46
 
 # phenoptrReports 0.2.11
 **2021-06-01**

R/reports.R

@@ -36,9 +36,8 @@ write_summary_report = function(csd_path=NULL, csd=NULL,
 
 #' Create summary charts from the results of an analysis
 #'
-#' Creates a Microsoft Word file or HTML report containing summary charts
-#' derived from an analysis. The file type is determined by the file extension
-#' of `output_path`, which must be either `.docx` or `.html`.
+#' Creates a Microsoft Word document containing summary charts
+#' derived from an analysis.
 #' @param workbook_path Path to an Excel file containing sheets written
 #'   by [write_counts_sheet], etc.
 #' @param output_path Path to write the resulting file.
@@ -57,19 +56,11 @@ write_summary_charts = function(workbook_path, output_path,
   if (is.null(output_path))
     stop('You must provide an output path.')
 
-  output_format = switch(tools::file_ext(output_path),
-                   docx='word_document',
-                   html='html_vignette')
-
-  if (is.null(output_format))
-    stop('Unsupported output format')
-
   rmd_path = system.file("rmd", "Chart_report.Rmd",
                          package="phenoptrReports")
 
   rmarkdown::render(rmd_path, output_file=output_path, quiet=TRUE,
                     intermediates_dir=temp_dir_by(output_path),
-                    output_format=output_format,
                     params=list(workbook_path=workbook_path,
                                 .by=.by,
                                 max_slides_per_plot=max_slides_per_plot,

inst/rmd/Chart_report.Rmd

@@ -2,8 +2,6 @@
 output:
   word_document:
     reference_docx: Chart_report_template.docx
-  html_vignette:
-    df_print: kable
 params:
   workbook_path:
     input: file
@@ -42,11 +40,6 @@ library(tidyr)
 knitr::opts_chunk$set(echo=FALSE,fig.width=10, fig.height=5.5, 
                       comment=NA, warning=FALSE, message=FALSE)
 
-# The default plot hook for vignettes creates a markdown image 'tag'
-# which breaks in pandoc if there are any spaces in the image path.
-# The standard HTML plot hook inserts an <img> tag which renders correctly.
-knitr::knit_hooks$set(plot = knitr:::hook_plot_html)
-
 workbook_path = params$workbook_path
 max_slides_per_plot = params$max_slides_per_plot
 max_heatmaps_per_plot = params$max_heatmaps_per_plot