better isolated generation of manuscript or via plan

MoseleyBioinformaticsLab · Feb 24, 2022 · 65af1b4 · 65af1b4
1 parent 95b37de
commit 65af1b4
Show file tree

Hide file tree

Showing 13 changed files with 37 additions and 14 deletions.
diff --git a/R/plan.R b/R/plan.R
@@ -354,10 +354,18 @@ the_plan <-
    pca_eval_summary = summarize_by_pca(all_pca_eval),
 
    single_core_perf = run_single_cor(),
-   complexity_figure = create_complexity_figure(single_core_perf),
+   complexity_figure = create_complexity_figure(single_core_perf)
 
-   supp_materials = render_docx(input_rmd = knitr_in(here::here("doc", "supplemental_materials.Rmd")), here::here("doc", "supplemental_materials.docx")),
-   supp_tables = render_docx(input_rmd = knitr_in(here::here("doc", "supplemental_tables.Rmd")), here::here("doc", "supplemental_tables.docx"), supp_materials),
-   manuscript = render_docx(input_rmd = knitr_in(here::here("doc", "ici_kt_manuscript.Rmd")), here::here("doc", "ici_kt_manuscript.docx"), supp_materials)
+   # add a comma after above target, and uncomment below if you want
+   # to generate manuscript as part of the overall plan.
+   # This may or may not be what you want to do.
+   # 
+   # Alternatively, you can do
+   #   source("generate_manuscript.R")
+   #   
+   #
+   # supp_materials = render_docx(input_rmd = knitr_in(here::here("doc", "supplemental_materials.Rmd")), here::here("doc", "supplemental_materials.docx")),
+   # supp_tables = render_docx(input_rmd = knitr_in(here::here("doc", "supplemental_tables.Rmd")), here::here("doc", "supplemental_tables.docx"), supp_materials),
+   # manuscript = render_docx(input_rmd = knitr_in(here::here("doc", "ici_kt_manuscript.Rmd")), here::here("doc", "ici_kt_manuscript.docx"), supp_materials)
 
 )
diff --git a/doc/ici_kt_manuscript.docx b/doc/ici_kt_manuscript.docx
diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_2_missing2cor-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_2_missing2cor-1.png
diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_3_leftcensored-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_3_leftcensored-1.png
diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_7_yeast_outliers-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_7_yeast_outliers-1.png
diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_8_brainson_outliers-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_8_brainson_outliers-1.png
diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_9_adeno_outliers-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_9_adeno_outliers-1.png
diff --git a/doc/supp_figure_count.rds b/doc/supp_figure_count.rds
diff --git a/doc/supp_stuff.rda b/doc/supp_stuff.rda
diff --git a/doc/supp_table_count.rds b/doc/supp_table_count.rds
diff --git a/doc/supplemental_materials.docx b/doc/supplemental_materials.docx
diff --git a/doc/supplemental_tables.docx b/doc/supplemental_tables.docx
diff --git a/generate_manuscript.R b/generate_manuscript.R
@@ -1,11 +1,26 @@
-# for the manuscript
-source("./packages.R")
-lapply(list.files("./R", full.names = TRUE), source)
-# we process the supplement first so we can refer to the figures and tables
-# in there in the main manuscript
-rmarkdown::render("./doc/supplemental_materials.Rmd")
-rmarkdown::render("./doc/supplemental_tables.Rmd")
-#beepr::beep(2)
-rmarkdown::render("./doc/ici_kt_manuscript.Rmd")
+library(callr)
+supp_materials = r(
+  function(){
+    source("./packages.R")
+    lapply(list.files("./R", full.names = TRUE), source)
+    rmarkdown::render(here::here("doc", "supplemental_materials.Rmd"))
+  }, show = TRUE
+)
+
+supp_tables = r(
+  function(){
+    source("./packages.R")
+    lapply(list.files("./R", full.names = TRUE), source)
+    rmarkdown::render(here::here("doc", "supplemental_tables.Rmd"))
+  }, show = TRUE
+)
 
-beepr::beep(2)
+manuscript = r(
+  function(){
+    source("./packages.R")
+    lapply(list.files("./R", full.names = TRUE), source)
+    rmarkdown::render(here::here("doc", "ici_kt_manuscript.Rmd"))
+  }, show = TRUE
+)
+
+#beepr::beep(2)